guess it mainly comes down to 2 things I think
1. we have no idea what powers/skills the cult has in regards to learning about ships without the blueprints
and
2. would our men and women giving/building the ships really have revealed military ship design without our approval/offering?
1. Again, not quite the same thing as modern blue prints at this point. Powers/skills, sure, didn't give explicit information. Fine. Okay. Setting aside that the source books note in multiple places how you can feel free to expand, change, alter the flat prayers given, sure. The canonical ones are things involving stuff like walking on water, pointing at a ship and making it harder to sail, pointing at a ship and making it an undying revenant no matter how much damage it takes, pointing at a ship and and explicitly gaining bonuses to navigation tests until whenever the ship reaches the next dock, pointing at a ship and making it lose all winds in its sails while also creating a moving sphere of calmed air meaning total protection inside storms as well, pointing at a ship and giving it winds that are perfect speed and strength for the journey, pointing at a ship and summoning rip tides around them, and pointing at a person and making them swim/row/sail better. As you can see, there are a whole lot of divine prayers specifically designed around ships. Rituals are known to be incredibly powerful versions of this, and while only two are canonically given, it is also noted that 'many more than these still exist in long-forgotten religious tomes'. The two in question are summoning a Divine Servant, like straight up Triton, or to consecrate a ground as truly holy, gaining further bonuses for all people of the specified faith on it. Extrapolating from the 'regular' lores, with rituals being the bigger mega spells that take weeks of preparation, one that helps them with learning a boat good doesn't seem too wild.
2. You're giving the ships in perpetuity/forever to the holy people of the seas. It just didn't seem like that big of a stretch to also tell them things if they asked, given how most coastal people in the Empire regard said holy people of the seas. This is Warhammer, and this is the Empire. Holy people have a lot of influence. The Grand Theogonist doesn't necessarily need to ask Electors or even local nobles if it's okay that he's recruiting from their population, he can plant a flag down and say 'join up for Sigmar' and people will literally just go and do that. The High Matriarch of Shallya could probably put her hands on her hips and glare and stop a border skirmish in Bretonnia between the Dukedoms. The Priests of Manann could probably just say 'hey, tell me about your ships', and people will do that. Or an Ulrican priest whipping up people into a frenzy to go knock some Sigmarite heads, all without permissions being asked by the nobles who rule over the people. However, unlike with the Cult of Ulric/Sigmar and their rivalries, and all that stuff, Manann, like Taal+Rhya, generally remain neutral. Things like Rutger aside, they're generally less of a risk of, I don't know, giving away naval secrets to others provinces, because that's simply just now how things go. It's not a foreign power or even a rival power stealing secrets, it's the Cult of the Water God who these people worship every day, and every moment they are on the water.
But I'll look again when I'm feeling less like garbage, and I'll probably revise it and make Frederick spring back from the keelhauling way faster or something, clean it up I guess, sure.