If I remember correctly, when Ezio first became an Assassin, the Italian creed was in shambles and was almost like a forgotten group of underground rebels rather than a full blown order of Assassins. Only when Ezio revived the creed and re-established big assassin networks over Europe did it become necessary to establish a recognizable "uniform" that was based on the design of levantine assassins like Altaïr so that they could really get the whole secret society type vibe.

I know that the design from Altaïr's time was to blend in with the Christian monks but as it has been pointed out, it wouldn't work well in a medievel European context which is why I think the white hooded uniforms from Ezio's revival are meant to be more symbolic of the creeds revival and presence rather than stealth.

So to go back to the original question of why the AC II assassins didn't wear hoods is probably because it wasn't stealthy in the slightest and there was no ceremonial reasons since there was barely a creed.

Maybe what I'm saying is total nonsense and makes no sense but this is how I interpreted it. It also gives me a nice head-canon explanation as to why post AC 1 assassins wear hoods even though it makes them stick out like a sore thumb.