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.