One has to remember that D&D is a strongly magical world, and there are a lot of little differences in the physics because of the magic. My favorite example is that cold and dark are not the absence of light and heat, but their energized opposites. A spellcaster bringing darkness or cold does not take away the light or the heat, but draws negative energy from the negative material plane which is itself darkness or cold.
Looking at the eyesight problem, in Multiverser terms eyesight is a body skill, and thus it continues to function normally despite the magic time stop. The physics of light does not apply.
The difference between stopping time for an object and moving extremely fast relative to that object lies in the fact that for any object for which time is stopped no change can occur. That's why you can't cut or stab such a person: he exists in a changeless state as long as the time stop is effected. You probably also couldn't dig a hole anywhere, because the floor can't be changed. A physicist would argue that the air is being moved by your motion, but the air is not "real" in that sense--it's not solid and we pass through it without being disturbed by it, so the fact that it is now "still" (in the sense that the breezes stop) does not prevent us from passing through it.
As to the missile problem, I never had to address it, but I believe that one approach is that when the missile leaves the control of the caster (e.g., the arrow leaves the bow, the bullet leaves the sling, or the dart leaves the hand) it becomes subject to the timestop and remains stationary in the air, and when time resumes it continues on its trajectory. Yes, this makes it possible to launch several missiles at point blank range at one target and have them seem to appear from nothing when the spell ends, but that's in essence intelligent use of the spell.
John, you also have to understand that with very rare exceptions you can't cast a time stop and use a bow--magic users are extremely limited in weapons available to them, multi-classed characters cannot advance to the highest levels to obtain such powerful spells, and a character with two classes (which is different from a multi-classed character) would take a long time to get there and have better ways to kill someone that that.
--M. J. Young