It depends on the usage, I guess. I have been using Emacs with its stock key-bindings for more than 10 years. I don't even remap my Caps Lock to behave like Ctrl like many others do. Yet I have never felt any issues due to repetitive strain yet. I do touch-type though which means I use the left Ctrl/Alt/Shift key while typing a key on the right side of the keyboard and I use the right Ctrl/Alt/Shift for typing a key on the left side of the keyboard. Maybe that distributes the repetitive strain evenly to both hands.
In the Emacs world, while remapping Caps Lock to Ctrl helps in reducing strain for many people, it also causes strain for some people. Every time, this discussion comes up in the Freenode #emacs channel, I have always noticed someone mentioning that remapping Caps Lock to behave like Ctrl caused them RSI.
Surprisingly, I did suffer from pain due to repetitive strain under the base of my forefinger once which seemed to be linked to overuse of mouse. The repetitive clicking, dragging and dropping in the Windows world nearly 10 years ago had taken a toll on my right hand forefinger. Taking inspiration from how we use keyboard with both hands, I then taught myself to use mouse with both hands (alternating between left hand and right hand every hour or so) and the pain gradually disappeared.
