The rule is 1 ship yard per colony with factories. The limit could still be imposed from earlier testing, it won't be there for the live servers.

Ship yards also are the only object that don't count to your object limit, but they do directly have an effect on your object limit. Normally it's +10 objects per ship yard to a cap of 1000 object, having more ship yard won't increase the object count beyond that, but it also gives you some wiggle room if someone goes around destroying your ship yards having more will keep your cap at 1000. ie. If you have 100 ship yards and someone destroys 10 you might still have 1000 ships with your real cap being 900 objects now. You won't be able to build any destroyed objects till you get your ship yard count up.

That's where the skill comes in that if you level up you get +10 objects per ship yard. So if you leveled the skill to the max level you would only need 10 ship yards to get the object limit of 1000 objects (Orbitals, and Ships are objects).

I know I went in to a little more detail about ship yards, but I thought it might help clear it up for new comers.