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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.
The EMH is never shown with pips on Voyager. The "ECH" was shown with pips appearing on its first appearance, however:
spoiler
The entire ECH subroutine was created as the result of The Doctor's daydreaming, so the visualisation of a rank appearing out of thin air makes sense in that context.The only other time the ECH mode was used in a genuine emergency (Season 7, Episodes 16/17), he did not have pips.