Maybe don't generalize your personal experience. Working with almost anything can give you carpal tunnel. Is there any evidence carpal tunnel is more likely then with any other input method?
More anecdotes from me on the input-method to wrist-problems correlation:
I weight train regularly. Lots of forearm tension. I noticed one day that it always hurt more when I was scrolling (using an original Apple Magic Mouse). Brutal repetitive strain injury. However, when I went for periods of time only using the trackpad in my MacBook, my arm would feel
Upon realization, pretty much immediately switched to a trackpad at my desktop as well, and problems went away.
It took about 18 months to get from "my arm really fucking hurts" to "yeah, it was the mouse". People always ask why I use a trackpad at a desktop, I tell this story. I don't remember the last time I used a mouse on my computer.
Many people, developers included, use the mouse to point and click when they need to change the caret position while editing text. If you do enough of that, the amount of precisely controlled movement involved quickly add up to repetitive strain injury on your hand/wrist. I've seen colleagues in their 20s/30s suffering from this problem, to a point that they needed to use the mouse with their other hand.
I'd recommend using the keyboard to navigate within a document. It's going to take some getting used to, but it'll be best for your hand health in the long run. Meanwhile, switching to a trackball (remember those?), a trackpad, or a trackpoint mouse, will definitely alleviate the symptoms.
I had a very similar experience. It started to happen within less than a year of starting my career. Both arms bothered me if I was typing in high gear for a long time, but the right was a lot worse and started to be an everyday thing. I switched the mouse from right to left side for a week and the right side started to feel a lot better. I ditched the mouse for a trackpad and picked up a kinesis advantage and never looked back. Still use a mouse and traditional keyboard layout for my gaming PC though.
How many years exactly? I am at almost 9 years of use and I have not felt the slightest hint of any problem (for reference I have in the past suffered from carpal tunnel related issues so I know what it feels like).