1) I seem to start out with alot of credits but towards the middle-to-end of my games, I begin running out of credits and that becomes the commodity I need (like crystal early game). Is there anything we can do other than civilian upgrades on planets to generate more credits. [Ignore upkeep please] Is it even worth-it to upgrade civilian structures on desert, ice or volcano planets that can only support a fraction of a colonizable planet?
You can exchange resources for credits on the black market.
Trading stations generate large amounts of credits, especially when you're playing as TEC, so build them if you've credits problems.
Lastly I always upgrade planetary infrastructure when I've enough resources and I know that the game will still last a while (some of them take long to make a profit).
2) Is the game still in beta or is it finished? I assumed because I bought it on the shelf that it was released but alot of threads have beta tags and issues mentioned in them.
It is finished.
The beta is of the new 1.1 patch which needed a public beta since it introduces some large changes (especially in balancing).
4) The gray lines that link planets become colored and the colored lines grow and shrink. I am assuming this is the influence of other cultures. Does this only or primarily affect alliegance?
Primarly alliegiance, secondarly a certain characteristic of your race (TEC, antimatter regeneration AFAIK for example).
6) Is the winning condition satisfied when all their planets are destroyed or when every structure is destroyed?
All planets destroyed, resp. all enemies surrendered.
7) Pirates are a mere annoyance middle to late game but can be held off for very long amounts of time with hanger bays and defense structures. Do you find you use a small army to stop them?
Mostly repair structures and turrets. Seldom a capital ship which needs to level up and isn't needed elsewhere.