The only real difference I have noticed, and Atapene correct me if I'm wrong, is to keep the side subbing into consideration when being on that wall.

If you're coming up along the sub-side, it will make it easier for the opponent to get fresh players in to stop you. They just have to go down. This will also be your benefit if you get a puck away from your goal along that wall. But as Liam said, only sub when being in posession.

Second disadvantage in my opinion is that inexperienced, over eager chief refs can call for wrong subbing when somebody sticks his or her head a bit too deep in the water to follow the game. They need to see 4 caps (or at least the top) above the water at all times.
It happened in Bari several times (but the refs were a bit of a joke there).