What happens if you Ctrl+C, Ctrl+V on the Doctor’s data files? Do you duplicate a sentient being?
In “Virtuoso”, Tom & Harry try to reproduce the Doctor but they’re basically trying to make him from scratch, so I don’t think their failure is relevant.
At the end of “Author, Author” we see many repurposed EMH Mk1s working as miners:
…and they seem to be self-aware, so I guess we have to assume that it’s technically feasible.
But then what happens if you Ctrl+Z?
I could definitely see people just taking it for granted that it’s fine due to the difficulty of pinning down one particular source of consciousness versus another. It isn’t obvious and everyone who goes through the transporter claims to feel fine, so unless they’re thinking a lot about their own consciousness why question it? Endless killing by convenience and ignorance.
Or, you know, not. Hard to say, though.