In my opinion, the simplest solution to the problem would be having sets of icons based on type of ship. For example:
I don't need to know the health of every fighter, bomber, and missile frigate in my fleet, so these could have small, simple, recognizable icons (that possibly merge slightly with an indicator of how many there are when zooming out).
The same (roughly) goes for my regular turrets. They're there to do damage in a battle, but I wouldn't need specifics on each separate turret installment during a battle.
However, for larger ships (ark, guardians, fortresses if those are still around, etc.), I need the play-by-play of what's going on, whether I have to move things around or retreat. These larger ships should have more information like the health indicator, a noticeable icon, and all of the other things, and this icon wouldn't really merge, or would merge rarely if there were very many nearby. However, because there aren't typically going to be hundreds of these in one place, you can make the icon larger and use more space.
Of course, then you get into the problem of which should go where. To that, I reply: build que. If it's significant enough to have its own constructor, it's notable enough for an icon (things like the minor faction ships in classic would be another story though, those are more fleet than special, IMO).