The Doctor was never intended to be a sapient program, and the crew take the situation seriously and treat him as a person when they find out. B'Elanna actually treats him as a person from the start, which I thought was interesting. It's not clear if the later EMH models are sapient, but the Bashir prototype didn't seem to be.

Mostly, the Federation seems to be shockingly unprepared for intelligent computers given how often they encounter them, like each time they think it's a fluke that will never happen again.

The sentient hologram idea bothers me. With Data they establish that consciousness is only possible with a specialized positronic neural net that is extremely difficult to reproduce. OTOH holograms are programs running in the ship's computer. Ordinary programs, on ordinary (for Star Trek) computer chips.

Voyager is often written as though a hologram has some special physical properties that make it logically different from a computer program without a holographic projection. But I think it's clearly established in TNG and DS9 that holograms are programs in the computer controlling projected force fields and replicated matter and whatnot.

I know The Doctor sometimes runs on the mobile emitter instead of the ship's computer. And TNG did break its own rules with Moriarty. And arguably DS9 did too with Vic Fontaine. I don't mind because these occasional exceptions are fun! The Doctor is the best part of Voyager! Mostly it bugs me when they imply that every computer program is sentient (but only if it's connected to a projector!); or especially when they bring in photonic beings that somehow aren't projections controlled by a computer and holographic hardware?

Maaaybe you could argue that Voyager holograms are special because the bio-neural circuitry has some of the same properties as positronic neural nets. But I don't recall any explanation of that sort in the show.

So is TNG's entire plotline with Moriarty. One could argue that the Federation knew about the sentience of holograms long before the Voyager era, and actively encouraged their slavery despite their clear sentience.

I know it's an aside, but this post raised this question for me: So, is Data still alive 900 years into the future? Can we get a Brent Spiner cameo on Starfleet Academy and FINALLY see Data and the Doctor interact on screen? I feel like they'd have lots to talk about in regards to the struggle for the acceptance of non-biological life forms

The photonic beings they encounter are right to be confused and horrified by the holodeck

The zeal with which Harry dispatches those goons shows you the kind of monster he really is.