That makes a lot of questions for a single thread...
I know at least one answer : AI is set to optimize its own star system, by colonizing every available planet, even if it's small. A little colony with just one facilitie is better than nothing. In small quadrants with lots of players, this strategy works fine.
If you chose to make no treaty with AI races, you will get no bonus resources, and your ships (especilly transports and colony ships) will be crushed by ennemy ships if they encounter any. And all AI will be more willing to declare war to you.
About resources shortages, my advise will be to not spend more resources than you have
.
Also use mothball and scrap old useless ships to save maintenance resources.