Do you recommend including them in your game set-up?
It depends on what you are looking for in the game. Having the minors in a game provides more options for diplomacy (e.g., buying/selling techs, establishing treaties, using them as proxies in a war.), economy (e.g., establishing trade routes with them), and military (e.g., conquering them).
If the major races provide enough options for you, then you can leave the minors out. If you want more, then the minors are good way to achieve that.
Are they there just to be conquered?
That's one of their purposes. However, as I said above, there is a lot more you can do with them, than just get a high-PQ world.
Can conquering them get you into diplomatic trouble?
Yes. Once you've conquered 2-3 races (major or minor), your diplomatic relations with the other races will drop, because they see you as a conquerer, and fear, that they are next.
If you add them to your game, why do you do so?
Primarily for the reasons above. However, I'm playing with my mod, Autumn Twilight. In it, I changed the minors to be able to colonise, and I also made them smarter. This means, that the minors are able to form small empires. Sometimes, they even manage to rival the major races. This provides much more of a challenge, and I find it more fun.