I am currently playing a 4 system map and have well over 300 ships, possibly over 400, and I've noticed that ship icons are disappearing when I zoom out, I can still see the models when zoomed in, but most of my arcovas don't show up when zoomed out, and although I'm not going to count them, I would imagine other frigate types share this problem. I have also noticed that a few enemy trade ships are not showing up. I'm about to restart the game to see if that works.
Also, I've noticed now and before that in large ctrl groups the number of ships fluctuates (not sure but I think hyperspacing ships don't show up in the group when hyperspacing. But everything returns to normal when everything drops out of phasespace. Not sure if this is a bug or intended.
EDIT: Restart didn't work. Still had the same problem. I also noticed that this problem expanded to include structures on other planets as well. It even expanded to the point where the planetary elevators things didn't show up, but atmospheric traffic did.
Tried to play using that, but at the first battle with my new fleet (took some screens showing the number of ships in it, but I can't seem to find the screenshots folder, where is it again?) my computer gave me a big FU and slowly combusted into a pile of dust until I ended the game, so perhaps it is actually my graphics card that is causing the problem (although I don't know why it would cause icons to disapper, seems more game related than graphics).
I believe my video card is a RADEON X300.