I think it's an arma limitation when comes to targeting. I shot 6 antitanks missiles on the ship hoping to bring down the ship by destroying the "guns", maybe only managed to get 1 while my wingmen took out the rest. So best to use your AI friend.. (a bit sad it wasn't me that did the hard work )
But I do agree if it's script-able (no idea how) to allow player to target those gun points ourselves will be much more satisfying experience.
If possible J_frost, can I suggest that some of the menus are hardcoded into the custom menus like (9 or 0 ) for action such as "gear down", "get out", "avionics" etc, having a pain trying to rearm without those action items.