I shop at a used-bike stores regularly. They are pretty knowledgeable but not antique enthusiasts. All of there bikes at the nonprofits come from community donations. I know of 4 nonprofits and another used bike shop near me. There was another but that was downtown and got closed by local hoodilums and the radicals of the big local bike club. It actually was pretty big news because the local radicals antifa types were vocal in promoting in taking the business owner and his lawyers out. The owner had oddles of trouble with harassment from the "homeless" and then the police more or less refused to help the with the crime problems that area is plagued with.
I don't think you should assume negative thoughts just be cause it is used merchandise. You certainly can investigate easily enough.
Did you ask the manager where he goes product? Have you talked with others that are knowledgeable of the vendor? Did you ask the police if there has been an complaints of the vendor? Certainly you have legitimate concerns, but you may be getting your imagination get the best of you.