Think about it, Kislev trade from north canal, Tilea, Estelia, Araby trade via Barrack Varr so Marienburg is left with not much at all that Empire can't give up.
It's a bit worse than just that, because being a trade-nexus is sort of a self-fulfilling, self-reinforcing prophecy; because there's a lot of merchants coming there, that makes it more attractive for merchants to come there, which in turn attracts even more merchants, and so on, and so forth.
The same is also true in reverse; if there's less merchants coming there, then that makes it less attractive for other merchants to come there, which in turn makes it even less attractive for merchants, and so on, and so forth.
Now, there's obviously limits and diminishing returns in both direction, but that still means that in case of a prolonged embargo/high tariffs, Marienburg wouldn't just lose out on the Empire's maritime trade, but that its own trade would suffer as well, as Merchants who'd normally seek out the city for its wide diversity of goods instead go to Erengrad or Barak Varr, instead.
Granted, it does probably hurt Altdorf Specifically more than it hurts Marienburg.
This is kind of an interesting situation, due to Altdorf's geographical location on the site where the Empire's northern and southern river-networks meet. So, if traffic to and from Marienburg gets blocked, then yeah, Altdorf would lose out, since any trade that would normally go towards the south of the Empire no longer needs to go through it, though any trade going towards the north still would.
However, that would then change again once the Kislevites' canal would come online, since then Altdorf would suddenly become the point where northern trade (ie, Kislev, Laurelorn, Ostland, Ostermark, Middenheim, Talabec, Karak Kadrin, etc) and southern trade (Tilea, Estalia, Border Princes, Barak Varr, Wissenland, Stirland, Averland, etc) would meet, turning Altdorf into a new trade-nexus.
So, in the short-term Altdorf would suffer a fair bit, but in the long-term it would benefit substantially.