Assuming the comma in the OP is inserted correctly, it differentiates the vocative you with the imperative mood from the indicative mood, which would not include the comma:
- You go to the store.
Some argue that the indicative construction can behave as an imperative where You functions as an emphatic adjunct of the standard zero argument:
- You go to the store!
Inserting the comma invites us to interpret You as the vocative:
- You, go to the store.
Regardless, you is the syntactic pivot of the sentence:
The syntactic pivot is the verb argument around which sentences "revolve", in a given
language. This usually means the following:
- If the verb has more than zero arguments, then one argument is the syntactic pivot.
- If the verb agrees with at least one of its arguments, then it agrees with the syntactic pivot.
- In coordinated propositions, in languages where an argument can be left out, the omitted argument is the syntactic pivot.
If we concede poor punctuation and parse the You as an emphatic adjunct, the implied you would be expressed in the adjunct, and arguing over "which" you is the subject argument of go is much ado about nothing.
Since the You of the first phrase is vocative, the implied you is the subject argument of go. Again, it is much ado about nothing, because the vocative you and the implied you identify the same entity.
Extra note: Some argue that You is an introductory single word phrase reduced from I am talking to you or You pay attention. They recommend punctuation that removes the ambiguity with two sentences:
- You. Go to the store.