Nuclear weapons are overkill, of course. I hadn't thought of that. Sorry, my moral compass is unreliable.
The possible arms race is also a good argument. Still, Starfleet ships should keep them in stock for emergency situations or when outnumbered. Furthermore, an arms race is already in progress due to the current Cold War situation.
However, I am neither an engineer nor knowledgeable about military technology. Thus, when the Admiralty, Corps of Engineers and/or the DTI have goods reasons to keep the 'sledgehammer' out of hands, who am I to argue? All I have to base my judgement are the FX from Endgame
Now that I think of it, Nemesis
would've had a pretty short battle with the Scimitar
were fitted with one or two transphasic torpedoes.