I dunno how this is in PvP so to avoid a firestorm I'm only going to meantion this regarding PvE targets. I've noticed that as soon as a ship like a BoP begins to cloak I lose my lock on the target. Theres no chance to fire a torp at the ship as it cloaks because its no longer selectable. The only way I've hit one while cloaking is if I've already fired the torp before the ship started to cloak.
I've also noticed that when uncloaking BoP shields are back up very fast. Not instantly but its almost impossible to get more then 1 beam hit on a ship before the shields go up, and thats if it decloaks right infront of you.
Again I don't know how this works or effects PvP so I'm not even going to suggest a PvP change.
Also I'm playing a Cruiser so I don't know if my sensors are playing a part in this. I hope its not my sensors because its been pretty well established that a Fed ship can fire on a ship that cloaks until it has completely vanished.
I think science officers have the ability to see through cloaks to some extent, so they may behave differently in that regard.
I have noticed that torpedos that are already on the way to a cloaked ship will 'poof' if the ship cloaks before they get there... I guess it means the torpedo lost target lock. Since the ship is likely moving when they cloak the chances of the torpedo still hitting are pretty low.