In portrait orientation they have the same orientation as pixels on desktop monitors, i.e. the subpixels of individual pixels are next to each other, not on top of each other. (I looked at my third generation iPod touch. Well, I took a macro photo with my trusty Ricoh GR Digital II [1]. The only tool I have with which I can make subpixels – barely – visible. Hm, water drops might work, too, but that seems a bit risky.)
I just checked Safari, they don’t actually do any subpixel antialiasing. Just “normal” antialiasing. I would guess that if it’s not used in Safari it’s used nowhere, so no problems with that :)
(Subpixel antialiasing seems unnecessary with resolutions like that. Heck, even any other kind of antialiasing is beginning to become unnecessary with resolutions like that.)