[>BKA< T Wrecks]

I dunno, I waypointed de_marrakech, and there is exactly the kind of spawn points you mention, but I don't remember being flooded with "no path to waypoint" messages. Then again, maybe I was just lucky...
And in the end, you are absolutely right. There are maps which make a "correct" waypoint system impossible, so the error display should have an option to be turned off. I think it could even be turned off by default, because 95% of all people use a bot for playing and not for waypointing - and waypointers are the only ones for whom this message is really interesting.