It makes a massive difference in comfort. 5 minutes typing at full speed on QWERTY and my wrists start to hurt. (I really don't know how people do it.) On Dvorak, I can type all day at full speed with no pain at all. Surprisingly, the keyboard hardware itself doesn't seem to matter.
(Details: I mostly use a Mac, with caps lock mapped to control, NSRepeatCountBinding set to ^u, and -- obviously? -- I rarely touch the arrow keys.)