Well, as otherd have said, both devices utilize the same technology. So, if you get headaches from the 3DS after a few minutes with it, you will likely experience the same result with the EVO 3D.
I have found that the 3DS does give slightly better viewing angles than the Evo 3D. With the Evo 3D, its all about finding that sweet spot. Also, on the 3DS there is a handy slider that adjusts the effect (depth) of the 3D imagery. So, if you are getting headaches, try adjusting that slider. On the EVO 3D, there is an option with each photo you take where you can adjust the 3D image effect.
I hope this helps.