Hi Ed - I'm afraid there aren't any anymore, although I think there still may be a basement shop in Little Belmont street which still sells vinyl. Haven't set foot in it for years, but it did used to have some records, but not a lot of folk / traditional music.
There's not really any independent music shop in Aberdeen selling our kind of music any more since "Bruce Miller's" closed a few years back. HMV on Union street does have a folk section, but that's probably it for Aberdeen.

If you have the time to go 15 miles south to Stonehaven, Peter Murray has "Celtic Chords", selling instruments and a large selection of traditional music CDs, probably the widest selection North of Edinburgh.
You may find vinyl LPs in some of the many, many charity shops in and around Union street - the Oxfam shop in Belmont street may be worth checking.
HMV, Oxfam and the shop in Little Belmont street are in the centre and all within about 3 minutes walk from each other.
If you're coming to Aberdeen for the "Button Box & Moothies" weekend, have a good time. Sorry I can't be there myself.
All the best, Kenny