The issue is not with the missiles, but with the AI. I have never seen a missile take out a bomb, primarily because the AI almost never targets bombs exclusively. With programming a point defense system, there can be ways for the AI to not worry about all the fighters, ships, and everything else before a bomb is targeted. This introduces a factor of game balance to the equation, but that's where the missile specs come in. Since AI cannot determine relative threat like people can, it seems logical to create this special case solution to fit the needs.
POST EDIT: WMC, if you can do that for an SEXP, you should be able to do that for a weapon flag, no?