Here's my theory on the subject, with two points I have noticed.
1 Both warships, and dropships use similar (but different) fusion drive technology.
2 Given what we know about capital weapons, aside from their shear mass, there is no reason a dropship couldn't use a Naval AC, or PPC. Any ship over 50k should be able to mount these weapons without any known problems.
My theory is that dropships use Duterium based fusion drives. Warships on the other hand use Helium 3 based drives. What we suspect of Helium 3 based fusion, is they (might) have better power to weight rations, and require far less shielding then Duterium based.
If everyone (out side of the wobbies, and the Com Star) assumes the drives are using the same fusion that dropships use, then the drives they create may not be able to power naval weapons effectively.
This however, fall short when talking about naval ACs. As I can't think of a logical reason why a large dropship can't be equipped with them as well as Capital missiles. Also I'm assuming that fuel is just propellant, and not needed to actually run the power plant of the either craft in question.