[Fyron]

"What effect on moral (or other) is there for establishing colonies on planets with different atmospheres?"

None. Colonies on all planet types and atmospheres function identically. The only difference is if you use alien population (primarily to undome foreign atmospheres), as they have a natural anger increase (towards average), instead of the natural anger decrease of native pop. This is trivial to overcome with a couple of police troops, though.

"Can a planet be terra formed , where the atmosphere is changed over a long period of time?"

Yes, you need to research Planet Utilization 7 to get the Atmospheric Modification Plant.

"Is there any way to know how many facilities any given planet has room for before colonizing that planet?"

Facility space in stock is always SIZE * 5, where SIZE is 1 for tiny and 5 for huge. If its going to be domed, divide that number by 5. If you have the necessary Advanced Storage Techniques trait, multiply by 1.2 and round.