I would doubt it. Flourishing excercises your fingers, which makes them more flexible and stronger. If anything, I would assume it prevents this sort of thing from happening. I'm no expert though, and I suggest you talk to a chiropractor if you're worried about this. Infact, I'll ask one tomorow and get back to you.
Carpal Tunnel syndrome comes with the excessive use of the wrists and the over-exertion of the wrists, it occurs in typists and pianists, I doubt it will affect flourishers... But in my anatomy lesson, I have learnt that the ulnar nerve controls the most of the palm and the fingers, so take care of that nerve. Heh.
I agree with Cory. Carpal Tunnel is from excessive use of wrist and finger muscles right? Flourishing is constantly changing which muscles you use depending on the flourish. I don't think you have anything to worry about.