I know this thread is old but am going to bump it anyway!
For Czech glass beads, if you aren't looking to buy in bulk, there's a lady who sells them in smaller quantity at the Havelske Trziste (Havel's Market). You can't miss that market if you're walking to Old Town Square from Wenceslas Square. When I first moved here, I went there a lot. She speaks English, German and Russian.
Miss Bijoux is located at Wenceslas Square (just a few shops from Debenhams). They carry a wide range of quality Czech beads. You can find some special beads (special cuts and shapes) but they're a bit pricey.
Star Beads is another place to go.
If you're a bead freak like myself, you may want to visit Jablonec nad Nisou. It's about an hour drive from Prague. I call it the home of Czech glass. I have visited the bead/glass museum and there are places where you will be able to see how they make glasses and beads. I believe you can get wholesale beads from there too.
Kotva (take Metro B - yellow line to Namesti Republiky or you can walk there from Wenceslas Square) is an old department store. That's where I normally get my yarns from.