Chemistry is a thing but it's largely reduced because baseball is a game based upon individual outcomes and not so much based upon teamwork like other sports. Even further, it's too difficult to quantify, especially as fans who are disconnected from the inner workings of the game. Therefore, it's mostly worth ignoring especially when winning seems to cure any chemistry issues that there may be.
Now if I'm a GM and I KNOW that a guy is a cancer, then maybe I avoid him or at least factor that in to how much I value him. Even then you'd have to be careful. But as a fan it isn't really something I care much about.