The Bosporus and the crossing in Italy and so on, are very small streches of water which can be crossed by armies with minimal difficulty (Darius crossed the Bosporus with an estimated 250.000 men by building a bridge out of small boats). So no real transport fleets are needed. The AI is pretty hopeless at naval invasions, altough a bit better with all the patches and so on, so this is why the land brdiges are vital for the AI.
According to the posts I could find, it is possible to block travel across land bridges with fleets, but perhaps the fleets need to be a certain size ? I used this tactic extensively in EU II, but I cannot remember if I used it in RTW. I think I did.