Transporting is blocked by shields, though, and that's enough to stop the weaponization of the technology. If you can defeat shields, you don't have to bother with transporters in the first place.
For whatever reasons, ships lack the power to keep shields raised all the time. With long-distance beaming, sensors become more important than weapons. Whoever detects the location of the other ship first gets to beam in their nova device. We know that ships can only be tracked over vast distances if you have the frequencies of their beacons but we also know that ships can be detected at quite long distances. You'd need an automatedd system.