They have been present, and they are noted, in canon, to act as a
force if they desire to.
The actor has existed in the background, but the actor simply hasn't had cause or course to act before. In canon, in the WHF universe, they are explicitly noted to have stoppered rulers before. It may not utterly destroy you, you still have a goodly amount of non-river/non-ocean based stuff, but it is a considerable portion of things regardless. Certain provinces like, say, the Moot or perhaps Averland, would be less affected, due to having far better climates and environs for internal development compared to rough and tumble internals of Ostland proper.
And the simple fact of the matter is that they didn't ask for an Elector's Seat. They probably could have gotten one. It is widely assumed [again, in Tome of Salvation or the
History of the Cults of the Empire Wiki Entry] that Magnus offered one to the Cult of Taal and Rhya, and they refused. Because that's the nature of their God and their Cult. But it's also acknowledged that Manann has never really utterly desired
love, but acknowledgement of his position and power. Through respect and healthy doses of fear. The Cult of Manann is often somewhat aloof from the ongoings of the Empire, remember that they jeered at Magnus when he came to Marienburg because he was trying to gain their support for a 'foreign war'. Maghda herself was largely unaware of what was happening back on dry land, right up until she had to directly and majorly engage with it. They are aloof and involved and wrathful and gregarious as it strikes them. But generally, they don't have the same rivalries that all the other Cults have. Sigmar/Ulric/Myrmidia. Verena/Taal+Rhya. Natural conflict points over things like progress and science versus nature or things like war vs. war vs. war god. And while there are other such minor Gods, the most utterly dominant of them all is Manann, and perhaps Morr. Marienburg itself was founded in Manann's name, much like Talabheim and Middenheim, meaning that it is both one of the oldest settlements in the 'Empire's generally agreed upon stretch of territory, and one of the most holy ones - for Manann. Manann doens't really scuffle with the other Gods, because there is no reason to. Sigmar is not the Heldenhammer, Destroyer of Goblins, Hammer of the Seas. Ulric is not the God of Winter, Wolves, War, and Waves. Every other minor river God is localized to that river, and are minor cultural touchstones that have almost no chance whatsoever of expanding from those limited locations and domains.
But Manann is the God of the Oceans and Rivers and Tides. Not 'a' river, or 'an ocean', but just straight up Oceans and Rivers and Tides.
It is by their very aloof nature that, really, unless you actually anger them, they really aren't that big of an issue for anyone to deal with, but when required they are capable of flexing considerable muscles when it comes to things that are within their domain. Such as river/ocean travel.
And Morr, while yes you face death every day on Mallus, you don't
hope to plunge yourself into situations where it might happen too regularly, if your the average citizen. Most people don't walk down to the saw mill, or open the bakery, begging Morr to let them live just one more day. Manann-related stuff? That's you stepping out into the water for your whole livelihood, every day, constantly. Dominant in their domains, but one has a lot more
active praying and sacrificing than the other, for the most part.
For instance, Dazh? Doesn't exist outside of Kislev, really. But
in Kislev? He has immense political power. Every town. Every city. Every stanista.
Every settlement has shrines set up to him. And while every settlement also has sections set up for Ursun, every
home in said settlements have images of Dazh. He is so colloquially worshipped and kept as a part of daily life that every single home has iconography dedicated to him. The Ungols have him stitched into their tents or carry wood carvings, even as they move about nomadically on the steppes. Everyone pays respect to Dazh, because he is the Sun and the Fire of the Hearth in one being.
And doesn't, generally, do much outside of that role, but is the sole one doing it.
If we return to the rivalries of northern fleets, not every ship is going to have a priest of Manann on it, least of all an Albatross Priest or Knights Mariner. And if there were skirmishes, that's ocean combat, and yet so long as both crews prayed to Manann and sacrificed some stuff to him on the way out, they're both able to smack around at least a little bit. Generally, though, the Cult of Manann
doesn't care so long as you make your tithes, do your prayers, and pay your respects to Manann. That's it. They have the Stormguard, whose entire schtick is hunting down the followers of Stromfels at all times, and the Foamborne, who go after the Holders of the Shore. They don't come protesting and blocking your people from hunting deer within a certain area of woods (like Taalites do all over the Empire) and they don't kill people for trying to burn books (like Verenans might) and they don't set out to ruin people that they think have 'gotten too big for their britches' like Ranaldians do on occasion. It's literally just pay respects to Manann, and keep your prayers and tithes up so we can try and beseech on your behalf when you set out onto the water, so that he'll cast a storm at the shore on another day, or that your catch is truly amazing and fills your net, or you just overall hopefully don't run into any problems. The issue with that is, a lot of the time, Manann's favor is things just
not going wrong, which is easy to mistake for nothing being done at all, but at the end of the day is simply not worth going 'and thank you Manann for ensuring that my fishing trip was perfectly and utterly mundane' is much easier, simpler, and a lot more times actually rightfully giving credit than you'd think.
But really, again, they canonically certainly have the influence to have gained an Elector Seat. But they clearly did not get one, because they didn't care to. The Grand Conclaves, where the Cults can come together and air their grievances on the regular, debating matters of all sorts and sizes, suits their purposes well enough.
At the end of the day, they are sort of an aquatic epitome of swim quietly and carry a big mace. They're happy to just go about their business, and it wasn't really until Karl Franz's time that it's noted that the Cult was starting to actually get a little
too entwined with command and control over commerce and influence in politics, but it's noted that a lot of that has to do with the Matriarch at the time ambitiously pushing exactly that. Which means that it took from the founding of the Empire, 1IC, to finally,
finally start getting corrupted enough to be spoken out against by
Marienburgers in 2522 IC. Considering the city they're based in, I'd say that's a remarkable amount of time before the character of the Cult was finally worn down to that point. So, yes, in 2522 IC, they were starting to more regularly flex the political and economic strength they have possessed, and people were getting a bit freaked out about it, because it was so unusual and uncharacteristic of them. Even people in the Cult thought that going such a direction was not really adhering to the wild nature of their God, and were getting pissed about it too. Marienburg had split off from the Empire by that point, but I'll bet with the wealth and influence they possessed, they could have asked for one from one of the Emperor's in the interim. Hell, the man who gave Marienburg independence could probably have been bribed by the Cult to give them a seat, but they just...didn't ask. Because they didn't want to.
I am sorry that you feel ambushed. While this is pretty concretely canon stuff, save for my invention of the Foamborne and the internals of the aquarium, the Cult of Manann is pretty much just...like this. I accept that not everyone has spent nearly as much (too much, some might say) time on the wiki, reading the sourcebooks like Tome of Salvation, and so on. I wouldn't call it a hydra disguised as a gecko, but more like you just...saw the top of the iceberg and not the rest of it below the water? And for most of the time, near as can be told in the source materials, that's how the Cult of Manann likes it. They have a considerable amount of strength that they just don't use very often, compared to how the Cult of Sigmar, Ulric, etc. throw theirs around on the regular. Taal, in canon, is sorta diminished because of his edicts making him get left behind by the progress of civilization. Manann has never, ever been so restricted. Like, the Cult of Ulric distrusts handguns and stuff, Taal distrusts black powder in general, Verena can never harm any knowledge, Myrmidia has to play by the rules, etc. Manann's stuff is like 'don't cut your hair and nails while at sea'.
But Manann, being the son of Taal, does indeed act a bit like his dad in general aloofness from getting
too involved in politics, most of the time and for most of their history at least. So their influence is normally just in everyday stuff, but vital everyday stuff. In Warhammer, that's critical to just Imperial life.
Right up until they feel the need to utilize that lower majority part of the iceberg.