With all due respect, I agree with Badger. In the first place, Arcen's whole design to go with the squads was to reduce the number of icons. If you're from AIWC, then you might be tempted to think that every ship will have its own icon. But according to the dev diaries, about 10 ships get an icon. Now, the capital ships sure do get thier own icons, but they're HUGE. I should hope that there will be plenty of clarity distinguishing THOSE apart from the rest of the fleet.
Referencing the final ks dev diary, there are a few points where Chris tries to bring in many ships. Sure, there will be many more than those ships on the much more heavily defended planets, but that's something to worry about later. For now, the clarity necessary is on your own ships, and then they'll fix the issues when it comes to the larger battles.
Final KS Dev Diary
https://www.youtube.com/watch?v=rr7R1lyF0Z4&list=PLc2dK5ROW0WBw47b5q2f_h0qB0a3Fgxhi&index=17At about 10:18, there are many ships on the screen. There are about 40 allied ships, and over 120 enemy ships. Of course, this is a rather moderate example, but there are certainly ways around it without such extreme (not that its all that extreme a suggestion in the first place) changes necessary.
Second Combat (Prototype Squads)
https://www.youtube.com/watch?v=VrhDQK9YnRE&list=PLc2dK5ROW0WBw47b5q2f_h0qB0a3Fgxhi&index=18At about 4:40, there are 100 enemy ships on the screen. Again, it's a moderate example, but I still agree with Badger; wait for alpha.
I completely understand your concern; user clarity. If I could make a suggestion, I'd ask the community and devs whether they think it would be feasible and clear to have the squad icons proportionate to the distance the camera is from the ship (up and down to caps, of course,) considering in the final ks dev diary appeared to have the icons the same size at all times. Maybe even inversely proportionate (smaller when closer, right?) so that they don't get in the way even when allowing a battle to pan out, zooming in to see all the pretty colors.
I've noticed that Arcen have listened to their community again and again, and these people are very creative. I'm sure they'll find a much better way to solve this issue that's a million times better than both our ideas combined, while retaining every bit of flashy polish marketing would desire out of this mechanic.
So, alpha, right?