Well, if you're talking about putting a 90-kT projectile weapon on a 150-kT escort, I think there might really be some recoil problems, especially if the 90-kT weapon is turretted and can face in arbitrary directions. Just rotating the weapon, if it has a non-circular turret or a long barrel, could change the center of gravity of the whole ship.
That was a side-point, though. Again, engineering is about finding efficient solutions to problems, and every decision generally has a tradeoff. It seems reasonable to assume that a huge weapon will be more efficient on a similarly-huge starship design, compared to a small one. Take the opening scene of Star Wars (episode IV) for example. Remember how the Imperial Star Destroyer had engines which appeared larger than the whole Rebel Blockade Runner it was chasing? Looks like those could also generate an immense amount of power which the small ship, given equivalent tech, could never hope to generate. Even if you assume some fantasy-tech devices which generate more power than engines, there is a lot more space, mass, and expense available in the design of the massive ship, compared to the tiny one. It seems pretty likely that the largest and most powerful weapons available will probably make a lot more sense, and work better, on the massive ship design. Not, perhaps, in ALL fantasy-tech, but in general, one would expect it to work out that way. If you want to model a tech that makes that untrue, SE4 of course allows it (woo-hoo!
), but all else being equal, I think if a single weapon is becoming a major percentage of the whole ship design, it's going to present some engineering disadvantages of one sort or another.
PvK