Can a bombing run be specifically targeted somewhere?
I was thinking if I could have my ship's bombers on the enemy plasma drives and retro-thrusters so boarding could be easier even for faster ships. (my ship is a grand cruiser)
Bombers being directed specifically to the engines
About as much as you can direct your macro-cannons to target the engines. (I.e., not by RAW but there's nothing preventing it that a creative GM couldn't handle).
Certainly it's possible; the problem (narratively) is that in order to hit a specific bit of a ship, a bomber will have to launch from closer in - meaning dropping further into the ship's turret's defensive envelope - and unlike an assault boat it's not doing so at ramming speed because it's got to pull out again.
I'd suggest, therefore, yes, but warn firstly you that it should be (a) much more suicidal for the pilots and (b) quite hard to achieve.
Second warning:
Most of the vulnerable bits of the engines...aren't. The bit of the 'engine' visible from the outside of the ship is the thruster exhausts. These are built to take having a plasma jet sufficient to accelerate a megatonne lump of iron, adamantium and ceramite at several G. A meltabomb going off in the tailpipe is just a warm breeze by comparison. Shots which punch through the hull into the engineering decks and go off there will definitely do damage. Throwing a bomb up the exhaust might well not.
My voidmaster was thinking of (in case the ship's armor is too reinforced around the engineering deck) piercing the exaust exits at one side in order to mess with the ship direction and also on its maximum acceleration. So the retrotrusters would be compromised with keeping the ship in the same direction (compensating the plasma venting sideways).
Well if a bomber was somehow able to drop a void torpedo inside one of those exhaust tubes would work, but for the most part hitting the tailpipes won't do to much. Honestly I can think of better targets if your GM is allowing precision hits. The bridge comes to mind, along with the geller field generator( if it is one of those mounted in the figurehead deals). heck maybe with enough DOS you can throw a bomb down a torpedo tube.