I have a black 3DS and have had no such problem. The circle pad leaves a little circle mark on the top half of the system (which is a very reflective black plastic), but you can make that go away by just wiping it with a cloth. No biggie. I really have no major gripes with the 3DS so far, except that the resolution is a little dated and the circle pad makes an odd clicking noise every so often for me (I think that might just be a defect in my system, since no one else has mentioned it). But those are by no means deal-breakers.
I didn't buy the 3DS for KH, but it is one of many, many reasons I bought it. I mostly bought it because I nearly always buy the all-new Nintendo systems (i.e. not the GBA SP or DSi), since I love the Mario, Metroid, Zelda, Professor Layton, and Fire Emblem franchises. Having KH too just sweetens the deal. I never have made it through OoT (I only ever got just past the water temple), so that will be the first big game I get. Then Layton, Kid Icarus, and Mario are just around the corner.
EDIT: The 3D is pretty cool, too. I usually keep it at about 3/4 strength, so that I have a little movement leeway, but I still get near the full effect. My eyes have never hurt, either.