Star Trek in general was shy when it came to using small atack craft. WWII showed us the importance of the aircraft carrier , if the ship had the capability it should have additional atack craft . history is screaming toloud to be ignored.
Trek space combat is usually more cinematically comparable to old-style battleship duels or submarine hunts than it is to aircraft-carrier style engagements with small craft as a big factor. Working backwards from this, if Star Trek consistently had its Federation and most of the other major powers declining to make heavy combat use of small attack craft for the battles that matter, clearly space combat in that era typically bears little resemblance to World War II.
A small number of fighters were put into use in the Dominion War; they, like runabouts and Data's mission scoutship, are even larger than Delta Flyer and won't fit into the shuttlebays of virtually any Federation starship I can think of aside from the
Galaxy-class main shuttlebay.
A runabout can deliver four full-sized torpedoes, albeit as "soft" launches only, a fighter can probably carry about the same, and I imagine Data's mission scoutship could carry a few more than that tops. Delta Flyer, AeroShuttle, and regular shuttlecraft appear to have no built-in method of delivering full-size torpedoes.
Full-size torpedoes are the only way I can imagine Trek small craft could hope to dent a Trek capital ship (aside, perhaps, from ramming). The phasers (and similarly-constrained Threat force beamed weapons) on a shuttle-sized or runabout-sized craft clearly present little threat to capital ships, and the small craft are not resilient enough to withstand much of a pounding (as their role in a Trek story is always to isolate the characters in a much weaker and more vulnerable vehicle than the mothership, don't expect this to ever change).
Defense of the mothership is thus a very unlikely mission for a shuttle unless, as you say, enemy small craft were involved; even then, it's unlikely these could really present a risk to the mothership (the bit where they transported the
Voyager main computer off the ship is an exception, and I think the little Suliban ships hit pretty hard for little ones as well), and I think you'd often be putting the shuttle crew in harm's way unnecessarily. Runabouts worked with
Odyssey against 3 Jem'Hadar attack ships on DS9, but reviewing the scene, somehow I don't get the impression their phasers were considered key to the effort.
For scenarios where the Borg were involved, I see absolutely nothing to support the idea that Seven and Be'lanna, or the whole crew for that matter, could have somehow upgraded the phaser armament on any of the ship's embarked craft to the point where it would have had significant utility against the Borg. It doesn't even seem to have been possible with the vastly more powerful shipboard phaser banks--
even for a drone using 29th century technology and inside knowledge against the Collective ("Drone").