I had explored this one, it was tough... I felt like asking for space travel, not only for ear piercing. I got used to Croatia and Serbia, every jewellery shop was doing that ear piercing with gun, clean and easy. Here you can find mostly that needle piercing way, or you have to go to the doctors to do this!
Finally I went to Bomton Radical Section (hair stylists for ultra modern hair styles, they are near Zizkov TV tower), they have piercing as well. I was happy with that service, it was a bit scary though, I felt like they were going to take my daughter and make her hair green and make a huge snake tattoo over her shoulders
Finally they just pierced her ears for 600kc or so, I dont remember now, it was before xmas last year.
Their web address: http://www.rsbomton.cz/studio.php?lang=en
Gun piercing I found only in one place, somewhere far away in P10 Strasnice, and I was lazy to go out of centre. Now I couldnt find that link, sorry.