Erm.... the same reason we today don't use nuclear weapons on every job that requires explosives?
We don't use nuclear weapons on a daily basis because of their unwelcome post-explosion side effects, e.g. radiation. As far as I know, there's no such issue with the transphasic torpedo. I wonder, why isn't the Typhon Pact also concerned about them? If deployed, Starfleet could one-shot warbirds.
Unless, of course, the technology is kept back because it hasn't "officially" been invented and counts as pollution of the timeline. Though, with these massive changes post-Endgame
At least they are in regular use in 2409, though transphasic torpedoes are not as powerful as they used to be.