What happens to the (alien) population if I successfully invade? Are they eliminated, or do I become an occupying force governing an alien population?
Will I be given a choice as to what to do with the alien population?
The surviving population automatically converts to your empire, there is no more resistance and rebellion is a function of approval on the planet, which can also be affected by your choice of
What are the pros and cons of using Information Warfare, which apparently causes very low casualties to the alien population but is very expensive to use, vs. Biological Warfare, which apparently causes very high casualties to the alien population but is very cheap to use?
No cons except the cost and the fact that it is not the most successful attack to reduce the enemy's strength. But it preserves infrastructures and pop.
Biological warfare is extremely effective, but it kills a lot of your population so the planets aren't immediately productive.
Are there any diplomatic repercussions to using any of the planetary invasion tactics, like in Master of Orion, where using biological weapons negatively affects your relationships with all other cultures?
No, unfortunately, you can genocide at will without any consequences. It would be nice if your relations with benevolent races were to be lowered substantially, but unfortunately, that is not the case.