The one inside the Deku Tree is story-relevant, so I wouldn't be surprised if that one was specifically programmed to NOT respawn. It would be weird for the Deku Tree to fall ill over and over again just because the sentient ulcer inside of him frequently reappears.
All others I've found so far seem to regularily respawn tho. If you want to know where their locations are, you can use this map and just scroll all the way down to the "Gloom Spawn" button.
(IIRC it is somewhat random what equipment the Phantom Ganon carries, so it might make sense to savescum until one with a sword shows up. I'm not 100% sure aboutt he randomness tho as I usually avoid those things if I can help it.)