Originally Posted by F = MA
First, maybe you should look for a new LBS, because the one you go to now doesn't know what they're talking about. You can use any shoe with any pedal - you just need the same cleat to go with the pedal.
Ah...no. You can't use any shoe with any pedal. My Nikes can only be used with three bolt look/shimano spd-sl style cleats period. Many of the shimanos only had the two hole setup not the three hole. So depending on what type of pedals the OP had...they may be limited to the type of shoes they can use. i.e. they are using a straight spd road or MTB type pedal (uses a two hole cleat)and the Shimano shoes they originally tried might on are only for SPD-SL or Look Style pedals (three hole cleat).
As to the OP...as long as the substitute shoes fit properly, are of a similar price range/quality and work well with your pedals you should be fine.