Just open your Wacom Tablet Properties and add Nuke as an application there, to be able to set custom preferences for it. Set the lower button to Middle Click and the upper part to Right Click.
That if your tablet is a Intuos or Cintiq, I think Graphire models don't allow you to change the pen button assingnments. Can't say about the "new" Bamboo but I guess it won't allow you to change that as well.
But I can be mistaken since it's been quite a while that I don't use any models other then the Intuous ones, maybe with the newer drivers lower end Wacom models (Graphire, Bamboo) gives you that option, I don't no.
As for changing those hotkeys inside Nuke as far as I know you simply can't.