As far as the individual scaling for technological advances, I do think there is room for some optional rules regarding scaling different methods of destruction from point to point on the tech curve.
However, as far as massive capital vessels go, I think the light offense (per tube) and high defense actually makes sense.
You should not judge the damage a ship can do on a per tube basis, but combined. Modern warships and some ideas about how capital starship fight, do not devote individual tubes/barrels to an enemy. They devote a battery. The battleship you mention will not hurl a 16" shell at a destroyer, it will at minimum hurl THREE 16" shells. It could if it wished combine it's turrets into a nine shot barrage of 16" shells.
Suddenly DEF enough to fend off a single 16" shell becomes woefully inadequate.
Now in Star Wars, capital ships engaged with what seemed like a complete lack of fire control. beams of light zipped away from them in all directions. Admittedly they were engaging fighters, but even in the scene were two capital ships got close enough to exchange fire with turbolasers, it was just a bunch of individuals shooting where ever they felt.
Star Trek on the other hand seems to combine attacks on capital ships. this could easily add excitement to a game. (just because the players are in a lightly armed freighter, if they have the teamwork skill and make their rolls, the two gunners can swing their turrets around to hit the armed corsair in the same genral spot at the same general time, and actually have a chance of not just puncturing the armor/shields, but to get in behind them and really do some body.)
Now to get the weapon to weapon comparisons to scale a bit more...