Black holes work how they want them to, without any logic, and certainly not like how we actually know black holes to work. If they want them to make time travel, they do that. If they want them to make things implode, they do that.
We're given the impression that if a black hole forms inside something (like Vulcan) it will implode. But we also see ships travel through them from outside. But somehow if one forms inside of a ship it's still going to travel through it? It's bad enough that the science is terrible, but that's not even internally consistent with the fantasy universe.
Since photon torpedoes can either blow up a ship or open up a temporal rift, depending on the episode, I'm not really seeing the problem here. Or, are you one of the fans I've yet to run across who hates Yesterday's Enterprise