Shield pas-through is a far larger problem than not. A single squadron of bombers making a single pass and taking out the shield emitters on any ship is, simply put, OP'd. The only way to deal with shield pass through and keep it from being OP'd would be to make bombers do such insignificant damage that they'd be useless. As is, if you don't use corvettes or fighters to screen the bombers, you'll lose your shields quickly and very quickly start getting your hard point ripped to pieces, but a single bomber squadron can't defeat a flotilla of ISD's by itelf. While it might not be absolutely perfect, the system the team is using is about as good as the game engine is going to allow for strategic play without making bombers insanely overpowered.