There are probably several but I know of at least two.
One is at the "Yellow market", cant really describe were. This is a huge market were especially cheap copies of clothes from Adidas etc are sold but the militaria shop was ok albeit rather expensive if I remember corectly.
The other one is located at the same street as Corona books, Hybernaska street.
The staff is very helpful.
Have a nice trip to Prague, Europes number one city for modellers imho!