Yes ships do build to fast. As someone pointed out in another thread, a colony ship with a cargo component holds approximately the population of Texas, yet it only takes two months to build, outfit and load the ship.
The other problem with production time is that planet population makes very little diffrence... small domed colonies should have signifigant penealties to production. (I have added this to the mod I'm working on, and it makes habitable worlds MUCH more valuable)
I think there is suppose to be a minimum population to operate one facility but I don't think it works. If there was a minimum population needed per facility that would give a big incentive to move your population around. It would also take a lot longer to get the full benefit of a new colony. As it is now I don't think there are any negatives to low population, just lower bonuses.
It is odd that a new colony builds facilities almost as fast as your homeworld.