Does this plugin affect my category list?

It depends on you.
Let’s say it can affect it, if you enable this feature, and also specify any of the categories for exclusion on the ACE Dashboard.

If I post in one category that is hidden, and another one as well, which is not. What will happen?

Then, your post won’t be hidden. This plugin only hides your post, if all of the defined categories selected for exclusion.

Does this plugin works with WordPress 2.3 ?

Yes it does :)

Does this plugin works with older versions of WordPress ?

Yes, it’s fully tested from 2.1 up to 2.3.3.

Does this plugin works for tags?

Not yet ;)
But the near future it will :)