Might we also roll this up into fixing another bugbear of sci-fi: that being large ships having a lower max speed than small ones?
The increased mass of a ship limits only its acceleration, not its top speed - and it would seem to be one of those facts of physics so obvious that I think it shouldn't be dismissed with 'rationalising too much' or 'this is sci-fi, live with it'.
Since the predominant reason for players caring about the speed of a ship is when they are in combat (either to escape or to chase down), and most moderate combateers use fuel injectors to gain an advantage, could we not link the ideas so that a ship of increased mass (over a Cobra Mk.III) needs to drink injected fuel at an increased rate - and can therefore only maintain the boost for a shorter period than a smaller ship?
This would still maintain the advantage of smaller ships having a greater chance of "getting away", yet not spit in the face of basic space physics (I know I know, it's a sci-fi game

).
I've heard of the 'fast-travelling pieces of matter' explanation as the reason for decreased top speeds for larger ships, but... really? There would be more hull to absorb the damage in a larger craft, so how would it be a limiting factor, provided that repairing such micro-damage is not being implemented in the game?
Why not just cap the top speeds, and as well as engines on larger ships needing more Quirium to jump, they also consume more to inject? As far as I can see you would still have smaller, less consumptive ships retaining an advantage.
And as Disembodied said, sun-skimming would have increaded importance.