My kid and I have discussed this at length. It's true, Bones and a few others live in a universe where they're the only soulful humanoids, surrounded by digital facsimiles. It must be depressing.
I'm firmly on the anti-transporter side, but I'm also super into the concept of artificial personhood. The people that step out of those transporters have just as much of a soul as the people who stepped in, even if they are separate people