I highly recommend Ceske Krumlov. The arms collection is very pleasing with matchlocks, wheellocks, Turkish arms and also a room of minting tools and you are allowed to photograph and take your time going through. Several cannon associated with the castle since the Thirty Years War are sheltered under a verandah.
In Prague Castle's Golden Lane is a display of armour that I think must be leftovers from the movies, but I could be wrong.
The Lobkowitz palace in Prague Castle has a lovely display of arms, and there is another in their castle at Nelahozeves. The amazing residence of Franz Ferdinand at Konopiste has the best of all, a huge collection of fascinating arms (plus his truly ridiculous amount of hunting trophies). But sadly these last two collections are guided tours only; you are herded into a room, it is discussed for five minutes, then the party is herded into the next room and the door locked behind. No photography at any of them.
I missed the museum of military history, but we were walking along the river when I realised I was looking at the massive brick faced bastion of a star fort. And I was looking for cannon, but saw almost none except smaller privately held ones.
I will post some pics later.