Hi Cas29
Is it like a strong wee smell? Have you ever found any dampness on her? It could be that she likes to sit in her toilet... Also I've noticed that when hamsters are a bit scared sometimes they let of an acrid wee-like smell. Did you leave the sandbath in her cage? Oh and is she longhaired??
I don't think that weeing in her ball is an issue, just because they cant really hold it in and not being in her cage she didn't really have an alternative.
I think you did the right thing taking her to a vet, just keep monitoring her. If she's happy and active in herself it might not be a problem