Hmm, I wonder if that's what the second mission was to find?
I played it on the CBM64, and seem to remember being given a mission to find a stealth ship. Flew around loads, but never found it as far as I can remember.
No, the Cougar is nothing to do with missions (in the 6502 versions, anyway - the other platforms have different mission code). It's just a rarely called part of the random spawning routine. Very rarely called.
The mission-related ship is the Constrictor, which you only bump into at the end of that mission.
I played it on the CBM64, and seem to remember being given a mission to find a stealth ship. Flew around loads, but never found it as far as I can remember.