Cats are not "clean" after they lick themselves, if anything this behavior is primarily responsible for the cultivation of a parasite lifecycle that has co-evolved to the cat's gut.

Cats, especially ones who share litter boxes, routinely get covered in potentially parasite-bearing feces via litter boxes and ingest it via grooming. This allows for easy additional spread/cross infection.

"Cats lick themselves, therefore they are clean" is a long-discredited but persistent myth.

The question was not "are cats clean," but "how do indoor cats clean themselves?"

Indoor cats clean themselves in the same way as outdoor cats, by licking themselves.