"If the enemy is in range, so are you"
The second the bomb-pumped laser is in range, so is inside the ships laser defense range.
It also raises the question of how effective a weapon the lasers are. Can it really top mass driver, particle accelerators and the like in raw damage? I doubt it.
then there's also the matter of cost.
Particle accelerators are c-fractional weapons. Mass drivers are even more feeble.
Lasers just by hitting at light-speed have an immense advantage in range as light-speed lag affects them less.
You're still right though: when the missile's in range to strike the ship, so is the ship in range to strike the missile. This is why wrote about the heat management difference.
This is why the acceleration difference could mean the end of manned ships directly engaging each other. The missile will be able to do at least a 100G-s (our current defense missiles can do this) and it is reasonable to expect at least twice if not three times that acceleration in time. Unless you redesign the humans themselves they would be limited to woeful 10Gs and that's very-very optimistic.
With a considerable light-speed lag acceleration becomes a very important question as it determines how big a volume of space you could be in the moment the laser (or even slower particle) beam reaches you. Bigger acceleration --> bigger volume --> less chance of a hit.
However you're right: particle beams and kinetic weapons are a lot more destructive. They also have a lot smaller "range" as they are slower. To achieve a hit you'd need to be a lot closer...
...and the closer you get, the better chances the laser has to maul you.
Armor incidentally is useless, as even fractions of acceleration would protect you better. Still since ships are limited by the humans they'd likely still mount some as advanced fusion torch drive designs tend to give more power than what humans could withstand. So ships would still take more hits to kill than a missile.
Initially while point-defense could handle laserheads through sheer difference in computing power ships would have a laser primary armament. When the missiles get smart enough - and actual laserhead X-ray laser nuclear warheads are miniaturized enough - ships will have to shift to missile heavy armaments.
The reason why I'm so high up on the laserhead is that it deals with several issues rather elegantly:
-It can be deployed far away from your ship, so your weapons are no longer in a single basket. It also ensures that the ship itself along with its crew won't be damaged.
-Even while being a missile (...and therefore possesing "unlimited range" if you're willing to put ballistic parts into their trajectory) it still wield a lightspeed weapon and therefore will pose the same threat to the ship like a laser equipped ship would.
-Since it creates the laser through a nuclear explosion it doesn't have to deal withe insane heat buildup that all lasers suffer from. (Ships using normal lasers would have around 20% efficiency. So you need to deal with four times the heat of the same energy as what you pumped into the enemy).
