Missiles, are meant to do explosive damage, that is the secondary use for them.
Personally, I always aim for the thruster of any fighter or bomber, take that out and he/she is dead.
Once me and Jinx I think back in 4.85 took both our SNACS out and we were pointlessly fighting each other.
Missiles are supposed to bring that extra bit of 'dodge em or be sorry' approach. Taking the hits either means you're ill equipped, or in the wrong battle completely.
Sub-system damage is part of the game, and I'll be damned if it gets taken away, if it does, I will have only 'pew-missile-pew' strategy left.