Personally I would go with the big bomber design you have, with an alteration. Swap out the size 8 box launcher for 2 size 4 launchers. Unless your missile design is astounding then it is going to suffer attrition from PD. Better to get lots of small hits through the net than hope for a few big hits.
That is not necessarily true... if you use ECM on the missiles that can sometimes make them equally hard if not harder to shoot down. A bigger warhead can also mean allot when you actually get through the enemy point defences. Even if smaller missiles generally get through more often does not always translate in needing less resources to beat the enemy.
Bigger missile also means better range generally which also can be quite important, shock damage is another important way to cause internal damage. At higher tech levels you also need ECCM or you are not hitting much with standard ASM missiles.
A smaller missile will leave your fighter more vulnerable to anti-fighter countermeasures... perhaps not against the AI as much but in multi-faction campaigns certainly an issue to contend with.
