I agree that the limit could be restrictive, especially if you are a combat person who has a lot of planetary defense. Your ships would end up being extremely thinned out and your insides would be defenseless as you try and expand outward.
An idea for a potential fix could be to have a 1000 unit cap on ships and another cap (maybe 500 or something) for the orbitals. Again, just an idea that could be implemented after we see how the first few games go.