I use them allot as I think it make sense both from an organizational perspective and a practical one.
If I have say a carrier battlegroup then the Battlegroup in and of itself only have the actual carrier in it (usually a sub-fleet in and of itself). I then have the Carrier Air-wing as a sub fleet which in turn are divided into fighter squadrons or strike groups and scout sections as appropriate in addition to sub-fleets categorized by fighter type. The fighter type sub-fleet is only for organizational purposes. For example each carrier group might then be assigned a color. So a fighter strike group may then be called SG-Green-1, SG-Green-2 and on another carrier SG-Red-1 and so forth. It is quite easy to just drag and drop what fighters you want to launch into a specific group when necessary. So I can have a few pre-made sub fleets called SG-Green-1, SG-Green-2, SC-Green-1, SC-Green-2 etc... where SG stand for Strike-Group and SC for Scout. Then I also know which group belong to a specific carrier group on a glance.
I then have each escort/scout class in their own section based on role and under them I organize the various ships and under them scouting and/or strike elements joined to the escort.
Any ship or formation you expect to eventually or at some point disconnect you should have in their own sub fleet. I'm not alien to having every capital ship in their own sub-fleet at times. I would just have the sub-fleet be the same name as the ship with some abbreviation of their role as well.
But I'm a sucker for meticulous organization of stuff so that is probably overdoing it at times...
But then again... using the sub-fleet system as a way to simply organize your fleets visually is very useful for your sanity, especially when a fleet can become quite big eventually.