fighters will get hit and explode
As you stated, in DS9 or TNG a hit doesn't mean immediate destruction, and even though a miss is an incredibly unlikely occurrence, a formation of fightercraft is only met by a very small number of these as such accurate defensive beams. So the main argument against fighters is that they for their part achieve very little, even in great numbers.
However, highly accurate beam defenses were already a feature in the 22nd century of ENT: NX-01 basically never missed a shot, and could actually fire more beams in a given length of time than her 23rd or 24th century counterparts. It would have been interesting to see what that ship could have achieved in anger against fightercraft, say, the Vulcan ones that got slightly hurt by the beam weapons of a shuttlepod...