Ok I see on the wiki their is for example bane generator and bane generator II, or scuge hoarding vault and Scruge Hoarding vault II, with a planet limit, Does the limit count for both or could I have a planet with for example Both 2 Scruge Hoarding vault and 2 Scruge Hoarding Vault II?

No, if there is a one or a two after the name, they fill the same slot in the DB so you are maxed at the total.

man that sucks The buildings are not sendable either are they? so like if you "upgrade" your buildings you can't even sell it on the secondary market for some CTP.....

You can still sell them, but the buyer has to alert a planet that you can take and place the structures on, and then the buyer can leave your legion and retake the planet with their new structures on it.