When you say "Have an apple" you are giving an order or an instruction. This order or instruction is an imposition upon someone, so we use the imperative mood. "You have an apple" is simply stating a fact - in this case, that someone has an apple - so we use the indicative mood (think about using your index finger to point at something). Hope this helps.
It would be redundant but not unacceptably so -- instead, it would draw attention to it.
For example, you might use it for contrast, as with "I'm eating a banana but you have an apple". Where in English we might pronounce "you" more strongly (but can't indicate that in writing).