Physical boardgames have this problem, too. Most impose a stacking limit of counters in every hex. Cardboard counters are opaque. So ... you can't easily add up how many combat factors are in a hex. You can't sweep your gaze across the board and see it in terms of a histogram of summed combat factors. You can't even keep track of your own units.
The physical solution is: long tweezers, and a great deal of fine hand motion. Or, you sideboard the entire combat, which means you physically shift all of the stacks (within a small region) to a side table with a ginormous hex grid, where every hex is like 3" on a side, so you can lay out a stack of 10 counters horizontally. Then sweeping your gaze works a little better (except that you still can't keep track of the sums). Your opponent will gladly cooperate by moving her own stacks, because she can't see hers either.
A computer-based game should leverage the computer to automate many of these mindless, "click-level" details away. I fully support the OP's idea of zoomed-out icons that carry tactical information. I'd go a step further and plea for (and write into my 5X, when I get to it) user-scripted icons, i.e. you choose your own icons (or import, or edit, your own), write a nifty lambda-expression or Boolean condition that teaches the engine when it shall be displayed (i.e. for what subset of the Cartesian product space of ships x modes x overlay hotkeys), and then the map gets labeled the way you want it. Then players (meta-)compete in the richness, conciseness, and usability of their information-displays.
I have deliberately designed ships whose ship type is well disguised, specifically to confound the enemy in situations as you describe. What happens to my clever "camouflage" if the game sticks little label icons on everything?
Sorry, but that's misplaced effort. This is not a camouflage-based RPG. The AI doesn't care (and cannot even know) what your ships look like; it must see every ship as pure numeric-field data, including all contents of the ship's Details screen (and not much else). (In fact, just imagine the kind of processing power you'd need to have a computer program "understand" a 2D image or 3D model. Before it could be confused, it would need at least (a) a dynamic memory of past seen-shapes, ( b ) the ability to see a new shape and classify it, and (c) an ability to guess what a novel shape is. Then you're relying on tricking the (c)-level reasoning to make it mis-classify a new shape. That's ... multiple Nobels and Googles, very likely a thousand-billion-dollar industry when it matures later this century, and probably NSA will hire you and lock you up with promotions you cannot refuse. You could use that to do automated bird censusing, or maybe fly it on a drone and label cars on the freeway in realtime, or scan crowds, or photos of crowds, and tag faces ... or build a home service robot that can interpret human facial expressions and gesture commands. No way would that kind of power make its first appearance in a game engine. I think you're putting computers on too high a pedestal.)
And most of that work is lost even vs. other humans. If I've got my map zoomed out to the abstract-icons level, my PC never even renders your models (nor my own). All I ever see of your ship is the numbers: its moves per turn, weapon factors, defense factors, and any pop or troops on board. You can't camouflage those, because they're disjoint from each ship's model. Ship design in GC3 is purely aesthetic, and has no effect on gameplay or ship combats. Enjoy it as an artistic pastime, but don't demand what it can't deliver.
The idea of tactical icons is a bookkeeping device to make the PC automate repetitive details for us. If it's in principle possible for us to drill-and-click one ship at a time and do our own summation, then let's just skip that rote work and have the UI display the summed histogram in the first place. Then we free our minds to play the game at the level of chess, instead of Qbert-with-the-mouse. Camouflage could be the basis of a completely different game, but not GC3.
In SE5, I don't camouflage my troop transports as enemy colony ships. Those really are (captured) enemy colony ships 
they work for me now
