Shouldn't the sentence "Have an apple." with an implied 'you' subject be a correct translation?
"Have an apple" is imperative. "You have an apple" is indicative. I think that's why the first form wouldn't be correct in this case.
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.
Would having "εσύ" before "εχεις ένα μήλο" be an unacceptable redundancy or does having "εχεις" already imply that you speak about the person you are speaking to, making "εσύ"more of an unnecessary word in that sentence?
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).