And also in a different way - when a real person really says "my mind was flooded with thoughts," (if that ever actually happens) there's often an implication that this person is overwhelmed - there's so much going on that he can't think clearly. In writing, though, this implication usually isn't there - it's more just a literal "I was standing there having lots of thoughts" kind of situation.
Primarily, though, the expression seems like a lazy attempt to evoke an emotional response in the reader. Like describing heartbeats speeding up and hands shaking and whatnot. It usually doesn't add anything, and it sounds silly. So go ahead - find a better way to say it :)