X 3 X a couple tournaments. It's a spree!
Too many details lacking for anyone here to be able to answer the OP's questions definitively. Did the players in question start the tournament? Did they finish a round or multiple rounds (that could/should be rated) before DNFing for the event?
Because there's a definite difference in how a player that registered but never showed up would be treated versus a player who began the tournament but failed to finish it. There's no official protocol (at least not that I've seen spelled out) regarding how to distribute any portion of an entry fee for a player that doesn't show at all. That's left entirely up to the TD. If the player completed a round, then I think the TD is obligated to list him and pay any associated fees to the PDGA.
The only real grey area I can see is a player who may have begun the first round but did not finish it. I've seen players like that listed in the results with all rounds 999, but I wouldn't be surprised if, with absolutely no scores to enter, a TD leaves him off the final results. I mean, how is a player that played 2 holes then ditched any different than one who never threw a shot? He gets no rating or points either way, so the player isn't losing out on anything if he's left off.
If anything, the only folks potentially affected by whether or not the player is officially listed are the ones in his division right around the cash line. And that's only if listing him versus not listing him affects the number of players paid out. Or if the TD included his entry in that division versus calling his entry general "added cash".
The concern about the PDGA missing out on a few bucks seems misplaced to me, and I'm all for the PDGA getting every dollar that they're entitled to.