I'm content to just leave it as unexplained. There's no evidence of a Queen, but by the same token there's no real evidence of Eggmorphing either. OK, so some people are cocooned curled up. So why aren't they turning into Eggs if they're being Eggmorphed? The Alien DC shows us the process doesn't take long, so at least some of them should be turning.
I'll be honest, the lack of explanation for more Aliens didn't really bother me at all.