I've never seen this sort of thing on bichirs, except on the operculum of wild caught polypterids, but never knew what it was.
If you do try drugs, you already know you're shooting in the dark, so an anti biotic drug like maracyn, maracyn2, or tetracycline are a great start, since most fungal infections are secondary infections to a bacterial one, meaning that if you treat the bacterial infection first, the fungal infection would be cleared vicariously.
That being said, I still have no clue what these pustule like structures are, but I'm willing to bet that with better care they'll be okay.
Are they eating?