This is impossible unfortunately due to natural reasons. Lagginess wouldn\'t be the only problem. Also the work for physics would increase exponentially (since for high speed collisions you\'d either have to cast the object (which is unbelivably expensive), or increase the sub steps of a physics update by at least 100 times.
Firstly, I want to make it clear that I have no idea how your physics engine works or why it would necessarily increase the processing load significantly.
That out of the way, this seems like a trivially easy problem to solve given that the game already takes the mass of a ship into question. My hypothesis (Massive emphasis here) is that the mass of an object would have to be calculated on each physics update to cause any issues with calculations involving it.
The simplest way out of this is to simply not calculate the mass of the ship when physics related operatiosn are performed. Rather, this should be calculated whenever the mass of the ship could change. This value would then be stored for whenever it\'s necessary in physics calculations. This can and will get jenky during combat with the mass of a ship can change rapidly if not handled properly.
From there, it\'s a simple matter of calculating a ships maximum velocity based on its mass and its accelleration based on its inertia.
Further, I\'d like to address this bit:
Players built huge ships with 3-4k thrusters, which made them pretty much invincible, since the ship had max weapons and unlimited speed (so you were unable to hit it).
Specifically the \"unlimited speed\" bit. If you actually had a completely uncapped speed, then this is, indeed, an issue. However, physics can rescue us thanks to Relativity. The amount of energy required to speed a ship of that size (3-4k thrusters is a LOT of mass) to any sufficiently advanced speed requires a lot of power. Naturally, as speed approaches c, the amount of energy required approaches infinity.
If thrusters push at a fixed rate with variable energy requirements - that is, they accellerate a given mass a given amount for an amount of energy that increases with velocity - we should, theoretically, never have an issue with ships traveling so fast that they cannot possibly be hit. Any sufficiently large ship would require too much energy to move at any great speed while smaller ships would hit similar soft caps.
To provide an example:
A thruster accellerates 50kg at 1m/s2 for 1 unit of energy (e) and has a mass of 10kg
A ship, without any thrusters, is 1000kg. To accellerate this ship at 1m/s2, you would need 25 thrusters (20 for the mass of the ship, and 5 for the mass of the thrusters) and 25e * Velocity to continue accellerating. Accellerating this ship to 10m/s would require ~9072000e
Thus, the energy required to increase the velocity of the ship 1m/s increases exponentially with the speed of the ship. Granted, this is a contrived example using far from balanced numbers, but it shows how such a system could work and could allow for theoretically uncapped speeds while still being fair.
The numbers would have to be heavily balanced, but the underlying equations should be sound. Mine was a simple Velocity! * Energy Cost, but a real calculation could use actual formulas (that I don\'t know offhand and are overkill for my example).