Um, if it's going at top speed already, taking out a single engine, assuming it has more than one, isn't going to slow it down. Engines are for acceleration. Technically, I shouldn't slow down when I throttle down in space. I should just coast, and for a long time. Virtually no friction.
Of course, that would mean that there's no real top speed for fighters. THey'd just keep going faster the longer you have the engines throttled up. To do what happens in Freespace and Freespace 2, retros have to be built in and tied in to the throttle control, logically. Well, at least for the throttle down behavior. It doesn't explain the top speed thing.
Really, the physics model in this game isn't right, but the fun is great, so who cares? The only thing I can think of that needs an accurate physics model right now is The Babylon Project, and they're making do without it.