speed is constant...and thus is writen in one of the INI files in your game folder. When you activate the game, game read's it and voila...what is written, is in game. Simple as that. Also...anti cheat program knows your speed before you even engage cruise, thrust or anything...
Since speed mod has several selections of speed it would be best that players who acctualy go 1000, 2000, or 3000 be banned automatically...However, those strange, pretty low speeds (500 or 600) should be checked out...People who want to cheat, who want to go fast, they would most probably use very high speeds...but when someone flies at 489, 556, or 623 (examples only) that could be a glitch in game.
Fact is that discovery as well as any other mod change the game in many ways. Since this game was made under Microsoft, i wouldn't be surprised of strange ways that can lead to these mistakes...
also..spinning, raming or any other way of accelerating your ship above 420 wont be registered...anti cheat doesnt meassure what speed you go..but what speed you can go...and like i said in the begining that info is stored on your computer in game INI file...