Learn Croatian: Kupuješ li cipele i čokolade? - Are you buying shoes and chocolates?

They are feminine nouns (cipela, čokolada) acting as direct objects in the plural. In the accusative plural, feminine nouns take the -e ending. This happens to be exactly the same as their plural subject form.

What if I was buying plural masculine nouns instead, like automobili (cars)?

Masculine nouns also take an -e ending in the accusative plural. So you would say Kupuješ li automobile? Note that for masculine nouns, this is a change from their plural subject form, which ends in -i.

How does Kupuješ li turn this into a question?

The little word li is a question particle used for yes/no questions. You create the question simply by placing li directly after the verb.

Where is the word for "you" in this sentence?

Croatian verbs change their endings depending on who is doing the action. The -š at the end of kupuješ already means "you" (singular). Adding the pronoun ti (you) isn't necessary unless you want to add special emphasis.