The problem with using powerbomb combos on Kraid is that you need to shoot him to get him to open his mouth, and then you have a limited amount of time to attack him before he closes it again. I don't think you have enough time to shoot him, charge up a powerbomb combo, and have the hits land. You might be able to use one shot of the combo to get his mouth open and use the others to hit him, but I don't think that'd be enough to kill him* and it'd almost certainly be slower than just pumping him full of super missiles (and ammo shouldn't be a problem because mini-Kraid can refill you).
* If I recall correctly, each shot in a wavebeam combo is equivalent to one super missile, and you need four super missiles to kill Kraid. I know there's a damage guide for Super Metroid (including health for all the bosses)
somewhere, but I can't find it. IIRC Kriole wrote it?
EDIT: well, I found
this, not what I was remembering but it does have all the relevant information. Kraid has 1000 health, and wavebeam combos and super missiles both deal 300 damage each.