Does my dog really have lyme?

If the vet ran a 3DX or 4DX on you dog it tests for C6 antibodies, they are not related to the lyme vaccine. It is a highly accurate test and indicates actual infection, even if your dog isn't showing symptoms he does have Lymes disease so, you can wait for him to show symptoms or treat him with Doxy for 30 days. I recommend treatment even if he isn't running a fever or in a lot of pain. Yes, every drug has a whole list of side effects but Doxy is not one I hear many complaints about, if your dog does react to it call your vet right away and let them know.