Fighters in HW1 are individual but you do get to use group formations.
Yes, its a pain (I was sooo very happy when I discovered STW with only max of 16 controllable units at a time :) ) but at the time that was the standard way of dealing with all unit types for RTS.

I am of course now going to have to go & run HW1 again, haven't seen it on the 24" LCD...

Another very good space RTS type game is Nexus:The Jupiter Incident, its got fewer ships but more detail/deeper level of control (& very nice looking ships too)