To do with not turning you into jam.
The limit in your speed is to help prevent physics turning you into flying mince. Even augmented and wearing a high tech flight suit, sudden stops and high G maneuvers would be very swiftly fatal.
There is a limiter built in to the ship to prevent you constantly accelerating until you reach speeds where an impact or sudden change in vector would be very bad for your circulation, skeleton, organs and other squidgy bits.
Similar to the retro thrusters, or lateral thrusters. Bad news if they were too powerful. Seat belt would act like cheese wire.
See the Expanse for reference.
The game doesn't have an acceleration cap.
You can start to black out around +40g and redout around -20 in ED, but otherwise, it's velocity, not acceleration, that is being capped. Even the redout/blackout limits can be exceeded without harm to our CMDRs. The fastest my CMDR's ship has impacted something and come to a dead stop without losing the ship is about 1500m/s and the fastest any CMDR has been going when stopped by a colision and survived to eject is at least an order of magnitude faster.