We don't use nuclear weapons on a daily basis because of their unwelcome post-explosion side effects, e.g. radiation.
No, we don't use them because we're not evil (hopefully) and don't want to take more lives than we must in order to defend ourselves. In most situations, they would be insane overkill and we'd be monsters to use them -- not to mention that it would bring down disaster on the world as other nations would feel compelled to use them to defend themselves.
The same goes for Starfleet. Standard policy is to avoid combat altogether if possible, and if it can't be avoided, to use precision fire against weapons, engines, and shields to incapacitate enemy ships with no more casualties than necessary. So obviously a weapon designed to stop the unstoppable Borg would be unjustifiably excessive to use except in the most extreme cases. Not only would it be stupid to use a sledgehammer when you're trying to use a scalpel, but it would provoke a proportionate response and create an arms race that would benefit no one.