I do quite a lot of typing on the N900 and the device seldom leaves my hands for more than a couple of hours a day. So all in all, I use the N900 a lot, and I don't suffer from any pains.

Using the Motorola Milestone for just over a week resulted me in having a bit of a pain in my left wrist because of the device's awkward keyboard layout. In comparison to this device, the N900 is very ergonomic.

Therefore I'd still investigate into what is truly causing this pain before pointing at the N900. However just like with any device or musical instrument, use the device with as relaxed hands as possible. Monitor yourself using the device. Make sure that there's no unnecessary tension.