Of course this will be happening. Heck some people feel bad playing FPS depending on FOV, etc. With 3D in all forms, cinema, TV, etc. there will always be people who find the experience induces this kind of reaction. The 3DS will be no different.
Unlike some other 3D forms 3DS could be even more prone to causing this if it's used while in motion for example, the combination of 3D focus with actual background motion - say playing in the back seat of a car - could easily compound the effect for some people.
Not sure what percentage of people you'll be talking about - but there will 100% be some. That's why there's a slider to adjust the 3D effect or remove it entirely.
Try to be reasonable... its easier than you think...







