So let's say there's a Ghost + Dark type pokemon and shedinja in a battle. We'll make Sableye an example. Sableye uses skill swap on shedinja. Bam! He can't be touched now. Can he be affected with Odor Sleuth to make normal and fighting types hit it? Then used any fighting type moves until he dies?
Please answer, or test it if you can.
Since you've got all the badges according to your signature, then yeah either remove the HMs or start all over again - Whirlpool being the least necessary buuut its special attack isn't that great so leaving Surf on there wouldn't really achieve much. So in other words, yes swap it for another Poliwag since you have something that can fly and you've used the HMs already.
Edit: Accelgor'd by Nica
I know the first quote has been answered by the two above, but I also wanted to add that for some reason Fire Fang is able to pass through Wonder Guard (in gen 4). Also if your opponent has Mold breaker, Teravolt, or Turboblaze, they ignore Wonderguard's ability.
Also this is from Bulbapedia:
So you can't even Skill Swap Wonder Guard.