Actually this is fairly common in games of this genre, that ships have a certain top speed, but collisions or other things can exceed it. First game that comes to mind is Star Control -- if you collide or go around the gravity well, you can go much faster than your normal top speed, and you stay at that speed as long as you don't use your engines. As soon as you start using your engines though, you start slowing down, back to your regular top speed.
In Starsector, the difference is that ships will slow down to their top speed regardless of if they're accelerating or not, unless they lose their engines.
If anything this is for immersion -- once you lose your engines then you lose control, and that includes your top speed, so that the ship really is out of control. And yes when you collide with other ships during burn drive, you risk losing your engines.
Counterpoint: It's hilarious when you only flameout half their engines and it just spins.
Also kind of funny when you hit them as they're retreating. I think the funniest though is when I don't realize that the Radiant I'm pushing around (to control where it might teleport) has lost its engines, and it ends up flying away from me...even worse when I was jetting my SO Aurora.