BC probably uses
CRC for this, not entire secure so to speak. While it should be unlikely that any random modification will give the same CRC, it's possible.
Seeing cloaked ships on the other hand, is more serious.
One big questions is, did it happen on one of your hosted servers?
If it did, then it's really serious. If they hosted it, then it might just be possible to hack it.
Could you e-mail me the mod in question (or a direct download link)?
Also, regarding the CRC, it's how they modded the demo, on which it's, more or less, impossible to mod (intentionally locked out).
[EDIT] I've been reading the thread mentioned, and saw the two videos on page 2, I'm not sure what I'm supposed to see in video 1, and in video 2 I see what might be a cheat (firing in the direction of a cloaked ship), but the ship doesn't get hit by it and explodes without reason in the end.
Could you also send me those attached images?