It isn't a shop, but an interactive museum where you can play (some of) the collection of instruments made in the workshop. There are lutes, guitar lutes, loads of guitars including very strange older body shapes. I don't think you can buy anything but it is totally interesting. It is called "Klang Holz e.v." in the Citadelle, which is beautiful.
I am not aware of any shops that specialize in early music and guitar. Dussman in mitte has a special sheet music store which has an OK guitar music section.
What are you looking to buy exactly? You can probably find some luthiers in Berlin who make lutes.