I think it depends on where you are shopping. Macy's and Sephora--yes, I expect their SAs might not know much about the scents and would consider a fragrance placed in the "female" section to be female and vice versa for men. However, most niche perfumers either mark their scents "unisex" or suggest that something might be more appropriate for a particular gender without making a big deal about it. Can't you just ignore what the SAs say and test what you like?
It doesn't matter to me what sex the scent is marketed toward--I wear what I want no matter what the designation. Today I'm wearing Knize Ten and I smell really good.