I know the Star Destroyers and Mon Calamarian cruisers don't have missiles, regardless of what the "essential" guide to ships says. They would've used them in ROTJ.
It's not too much micro-management for fighters to fire missiles, more than it is for them to fire blasters. I can picture them having some sort of rocket system. They attack large ships with torpedoes and lasers until they run out, and then attack with lasers only.
Similarily, A-Wings would attack with concussion missiles and lasers until they ran out, and then it was lasers only.
I guess it'd be an idea to have a key to press that toggled whether selected units fired their missiles. I wouldn't want to have my Y-Wings drain their torpedoes taking out an enemy interdictor when I know they're about to face a Star Destroyer.
If squads of starfighters are 1 "unit", and if you have a system similar to Generals, it wouldn't be much of a problem. (What Generals does is give you three icons for USA as to which kind of drone you want to add to your units if you want. Just click it, it builds and adds it?)
I hope you won't be upgrading your units during battle. More likely, your adding special stuff to them out of battle. Ideally (in my opinion), nearly every unit/squad would have some sort of special weapon and/or equipment. Infantry squads could get a deployable E-Web, X-Wings could get torpedoes, and so on.