What happens to Eb or other characters that I don't want to add yet in my party?
Can I recruit them later? Does the game have a main hub zone like Pillars of Eternity?
Not sure about all of them, but I know that some of them definitely allow you to recruit them later (Lantry sends you a missive in act II if I'm not mistaken). If you want to be 100% certain to not miss them (unless someone can definitely verify they can be obtained later), it's probably safer to just recruit them when you first see them (if you're over your party limit, you'll have the option to swap out one of your party members - you're under no obligation to add them to your party immediately though).
In the case of Eb, I'm not sure since most people who don't recruit her end up killing her instead. So she might disappear for all I know.
At the end of the first act, you will get something similar to a home base or hub - all characters that you have recruited will hang out there, and that is also where you can change your party composition.