Maybe I'm just old-fashioned but I was under the impression that energy bombs were coded to the frequency of the drive on your ship and programmed not to emit an compound-expanding energy field on that specific frequency when they detonated. This means that in the actual event, when you had to launch and leave this way too expensive "final solution" to your woes, all of your enemies went boom-splat and you didn't.
Of course, that is merely my suggestion. I believe that Energy Bombs are rather outdated weapons designed for one reason only - to make pretty patterns in the sky when detonated (to para-phrase Kelly's Heroes) and if deployed should do the following: (a) blow the living crap out of everything with the exception of your own ship, (b) leave a degree of debris in their wake with the size of that debris depending on the distance that the effected item or ship was from the center of the explosion. This debris can be anything from escape capsules to cargo to hull debris, all scoopable. I see no reason why we can't recoup some of our losses when we use one of these.
Alternatively, we can "mark" damaged ships which are dead in space and unmanned with a tag which declares them "salvage" and get a bounty for them after we've blown the living crap out of them.
Love DARK STAR ... however there are two distinct versions, one of which I like and the other which I hate, either way neither of them is released on DVD here in the U.S. because the bleeding heart liberals got upset about soe girlie pictures on the walls in the quarters (a converted cargo hold).
Dark Star is a good reason for not allowing A.I. to get too smart in my opinion! However, that said, why don't we simply upgrade Energy Bombs to difference classifications? We can have the BLOW THE CRAP OUT OF THINGS version, the BLOW THE LIVING CRAP OUT OF EVERYTHING version, and of course the AW, TO HELL WITH EVERYTHING ... GOODBYE CRUEL UNIVERSE version; each of course costing more and more money. The cheaper the bomb, the less damage it does. Then of course, we can have one called the "twenty minuters" (20) gettit? D'oh!