In my experience, nerve compressions such as ulnar nerve compression or carpal tunnel syndrome arise from incorrect typing posture and the use of wrist or arm rests while typing rather than from the use of any particular type of keyboard or mouse.
That said, I like typing on a HHKB Pro 2, which has case-mounted Topre switches. The case-mounting provides more resiliency than plate-mounted Topre switches as found in, for example, Realforce keyboards. I use my HHKB with both Windows and Linux machines.