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Because of his original purpose, it makes sense that the Doctor wouldn’t have held a Starfleet rank during Voyager.
However, in Prodigy, he still doesn’t have pips. This leads to my questions:
According to the STO wiki, he doesn’t wear them by choice but does have a rank. That might be a reasonable explanation; I can’t imagine Janeway not at least trying to field commission him.
There's an argument to be made that that changed the moment he started to be established as a sapient individual of his own.
It bring future Federation technology bequeathed to him may help there too. The Federation likely doesn't want to risk issues with the Time Police by confiscating and studying the emitter, so just let him keep it to do with as he wants.
There's also an ethical argument that removing it would severely restrict his ability to move, given that Starfleet would have trouble furnishing him with a sufficient replacement.
We also know from Prodigy that the Voyager was intended to be shelved for study, so it no longer being active might also be a good reason to allow the Doctor to roam about, instead of effectively trapping him on the inactive ship while Starfleet scientists pulled it apart and studied every crook and nanny.
Actually, according to LD:Twovix, didn't it become a museum ship?