I've never had any wrist problems since I moved to the sales floor (and I have pretty twingy wrists), but that's probably because I stick to the LPDA's and only use a PDA on rare occasion. Those things are heavy and awkward; I can see how they could do a number on your wrists!
Suggestions to help alleviate the problem...wear a wrist brace, perhaps? It will give you added support and help keep your wrist from bending or flexing excessively, which is what causes carpal tunnel. Other than that, maybe make a conscious effort to not overwork your wrist and to use it properly...your wrists, just like your back, neck, etc., needs to use proper ergonomics and technique otherwise you're just straining muscles.