And here is the problem, because the empire absolutely would suffer huge problems, the reik is very much bigger then the canal, can take more ships with more cargo going a more direct route.
Should the empire decide to blockade Marienburg from the inside then Marienburg would still have trade with bretonnia and kislev, reduced in total but not cut off.
The empire would also have trade, but absolutely massively reduced because of the increase of how far one has to travel.
Just because one can now go around Marienburg doesn't mean one wants to go around Marienburg.
The difference in distance is completely irrelevant; in our world ships preferred to travel an additional ~8000km around Africa, simply to avoid ~120km of land-travel over the suez isthmus. The additional distance ships would need to travel to access the Empire through Erengrad instead of Marienburg is pretty much nonexistent by comparison, and for ships from Tilea, Estalia, Araby, etc, the Barak Varr route would now be shorter by default.
The difference in throughput for both Reik and Canals is pure guesswork, but for the sake of your argument, let's say that you're right, and the canals being built could handle only ~50% of the trade volume that's currently going through Marienburg for some reason. So what? 50% is still vastly better than the 0% trade the Empire would otherwise have available whenever Marienburg feels like screwing them over, and in return for that reduction, Marienburg would lose ALL of the Empire's maritime trade with Kislev, Bretonnia, Estalia, etc.
But that ignores that the Black Water canal is being built by
Dwarfs, who're kind of known for their penchant of over-engineering things, so I kind of doubt that the canal would be anywhere near the bottleneck you expect it to be. And if there is enough demand for the canals to become bottlenecks, expanding them is always an option.
So while the Empire placing an embargo on Marienburg would definitely hurt them in the short-term, because existing trade-routes would be disrupted and need to readjust, in the long run they'd be perfectly fine with trade now moving through those canals, while Marienburg would suffer.
Yeah, partly because the Marienburg navy is somewhat of a match to the empire fleet.
This is another factor that the canals change; IIRC right now the Empire's 2nd fleet is stationed in Marienburg, partly because only Marienburg has the facilities for them, and partly because, as much as the Empire hates Marienburg, it's currently still reliant on it for maritime trade, so the Empire's obligate to defend Marienburg against naval raiders out of self-interest. With the canals, defending Marienburg is no longer a strategic necessity for the Empire, so they could easily decide to relocate the 2nd fleet someplace else.
Which in turn would mean that, to maintain the same level of protection, Marienburg would now need to spend its own money, which is money that couldn't be used for trading, or playing fuck-around games with the Empire.