Hi there!

This one is a little better, because usually after cutting thrust the speed returns to 0, but I am still able to far exceed the speed limit for the Llama.

When starting a new campaign, did a repair and refuel and then pop off the planet.
Aim at Serenity, and accelerate to full speed. (125)
Now, at a fairly slow rate of turn, turn 180 degrees so that serenity is behind you. If you see the same issue that I am seeing, your speed should touch roughly 300.

In the classic versions of Vega Strike, this was simply impossible, and your maximum speed in MANEUVER mode was always pegged at 125 for the repaired Llama, and whatever other speed was set if you are flying another ship.
For all ships, the maximum speed that you could get in a straight line was also the speed that you got through a turn.

With this branch of the game engine, and the master branch of Assets there is a save file which I basically did the same thing. New campaign, and repair and refuel the Llama. In more than one instance, when loading this game, I was able to do this turn and cut thrust and the ship continued at a speed of 300+

To re-iterate this in maybe another way. When you have your flight computer in Maneuver mode, it decreases the thrust from your main thruster while you are maneuvering to ensure that you never exceed the maximum set speed.
As I mentioned before, you can easily turn off this functionality by setting the flight computer to travel mode, and then your maximum speed is much higher.

Hmm, maybe I can put it another way.

The top speed in maneuver mode of the flight computer is similar to a electronic speed limiter in a car.
When you accelerate in a straight line with your space ship, maximum thrust is applied until you hit that set limit, and then thrust is cut to maintain that speed. I think there is some simulated drag in Vega Strike, but it should be minimal.

Now when you change direction, a combination of your thrusters are used to change the course of the ship.

The thrusters pointing in your previous direction of travel will fire to slow you down in that direction, and the other thrusters at the back of your ship will only fire enough to keep your total speed to whichever speed was set.