The smell that may be offensive to your nose may be one that your pup loves—and remember the opposite may also be true. Doggie perfume may be something that your pup finds bothers her sense of smell or allergies. I think the best bet is to find a happy medium that is not offensive to anyone.
Also, are you brushing her regularly? I find that when I keep my Jack Russell’s on a regular, daily or every other day, brushing schedule his coat seems shinier and less funky.