"Do you have the headphones?"
Translation:Ovatko kuulokkeet sinulla?
"Do you have the headphones" is inquiring after specific headphones (as the "the" implies), thus, "Ovatko kuulokkeet sinulla."
"Onko sinulla kuulokkeet?" is more asking if the other person has/owns any headphones in the first place, and I think in this case you could also use "kuulokkeita" instead of kuulokkeet".
Someone else might be able to explain this better, but I hope this helped a little. ^^
Yeah, "sinulla" is not the subject of the sentence (even if "you" is the subject of the English sentence), "kuulokkeet" are. In other words, it's the headphones that are on/at you.
"Kuulokkeet ovat sinulla" - You have the headphones. (lit. The headphones are on/at you)
"Kuulokkeet ovat pöydällä" - The headphones are on the table.