Ad monastery - I think Viera meant the
Brevnov monastery. It's the oldest monastery in the country, founded in late 900s, but architecture-wise it was almost completely rebuilt in the baroque period so it doesn't look
that old. But yeah the monks run a medieval-ish looking "pub" there where you can have all kinds of old Czech meals, I think they even have their own brewery, but I don't know for sure, it' been some time since I went there. It's not strictly speaking in the historical center, but it's pretty close, just take tram 22 that goes through the center, direction "Bila Hora" (not "Hostivar") and take off at "Brevnovsky klaster" which literally means Brevnov monastery. It should take like 15, 20 mins from the center.
Ad museums - I am not aware of any specifically military museums, but maybe there are some. There's always the
State Institute of Military History that has some expositions. So maybe check them out and see if they can point you to something more specific.
Ad pickpocketing and Nigerians - yeah if you survived Moscow and Petersburg, Prague will be a breeze.But i felt obligated to left a warning for posterity
Ad pubs - I wouldn't say any of them particularly hipster places. Chocobamba is sort of headquarters of the politically incorrect hip hop/horror-core scene, but the people there are mostly working class kids who drink a lot and smoke a lot of weed and rap about dead girls in the cellar and stuff
The last thing it is, is pretentious.
Alternatiff, despite its name isn't really all that alternative. Again, mostly working class people with tattoos in camo pants who like to get high.
Weed is relatively easy to get, sometimes the dealers like to be difficult and tease you for 15 minutes that you are a cop, but since you will obviously be a tourist, they will probably skip the part
I'm not sure if pointing you to specific places would maybe constitute breach of forums rules, so...