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Are clear on the driver's side. The rear one on the passenger side has one of the hat channel running under it. The floor boards were replaced before I got the vehicle, so I'm not sure if that was a misplacement on the part of the previous owner or not. At this point, should I just drill out a hole in the hat channel?

If you don't care how quickly the old girl's metal starts to corrode then just drill right thru it. Otherwise fix it by correctly by re-positioning the floor skin and the hat channel.

The hat channels are tack welded on, right?

Spot welded originally. Since someone has done a half/arsed floor replacement you'll have to look close to see if the spot welded or ran continuous seam welds.

Many are old and rusted out, so I got a complete set of hat channels awhile ago, I just need to paint them. The only new hat channels are the ones the rebuilder of the jeep put on the two front floorboards. It might make sense just to pull off all the hat channels and replace them, seeing as to how I have a complete set. What was the purpose of the hat channels in the first place? To reinforce the floorboards?

Yes