While the speed limit officially is 100m/s, a player can go 110m/s which makes sense to allow a player to move around a ship going at 100m/s. Objects can also fall up to 104.38m/s into gravity.

Well I think this is a minor mechanic that can be small enough to implement with little issue, while being worth it to do, if my understanding of how speed in the game works is right. In games like Freelancer, you could use afterburners to temporarily increase your ships' speed, but this increase would only work with the afterburners on and when not using them, the ship would return to the regular non-boosted speed.

Well the idea is, maybe so long as your thrusters are still thrusting the ship can exceed 100m/s, maybe for instance some speed between 100m/s and 110m/s, maybe that number is also somewhat dependant on the thrust override level too, but killing dampeners and otherwise coasting would not allow a ship to go past the 100m/s limit and the ship drops back down to it. It would also give a more satisfying reason, with feedback to the player, for pushing their thrusters to the limit even though their speed would otherwise be maxed out.

This would also have an effect on gameplay where players onboard an over-speeding ship would feel a 'perception' of acceleration in having to try harder to move forward relative to the ship's direction of travel than backwards, because of the player's speed limit of 110m/s.

In terms of how AI works, AI blocks will not exceed 100m/s anyway, but maybe an option for over-speed can be added for the purpose of things like missiles to still work.

To give this small mechanic more depth, a steep curve in power needed to get to over-speeds can be implemented, i.e. maybe it takes twice as long to get from 100m/s to 101m/s as it does to get from 99m/s to 100m/s, then twice as long again to get to 102m/s etc. This way, there's a good but balanced reason to design ships which accelerate fast and it gives just a bit more differentiation in 'speed' between big huge ships and smaller ships. Allowing smaller ships to better eek out full-speed pursuits or escapes, even though technically they are bound to the same limitations.

If you wanted to get REALLY cool with it, extra effects like camera warping and shake can be added as the ship goes more and more into over-speed while thrusting.