I may be very naive, but all the LP Juniors I've ever seen have only one pick-up - I think you talking LP Specials!
Whatever has happened to the guitar in the store is not how the factory intended it. You may be right to avoid it, but I have been sick for 30 years that I passed up an Epiphone Sheraton ca. 1966 because one pickup was not performing properly. I've got to say that LP juniors/specials are very overpriced, but a good one is a good thing to have. If it plays right and sounds right and it's what you want, buy it and either work out what's strange about it or pay someone else to do it. The man in the store reminds me of the caption to a Kliban cartoon - "But of course, Dublische Torte make you sick, sir -Dublische Torte SUPPOSED to make you sick!"