I am also having this issue. Even though having the dwarven runes would not be that useful in the long run, I still want to know how to obtain them just for the sake of completion.
The main theory that I have is that it's just a bug. When you get the keys from Snatch and return them to the guy who makes steel bars, it seems as if he is about to give you something, but never gives it to you. Then, when you talk to him again, he says something completely different while most NPCs would just repeat their last line.
Other theories include:
1: They could be located in the locked chest south of the town. I have yet to open this chest, but on my next play through, I will try and open the chest while still in possession of the stolen keys.
2: They could be north of that statue-barricade, which I have no idea how to get past.
So, a little help would be appreciated from anyone who has discovered them

EDIT: If there is anyone who is out there who has... MaxCoderz has turned into such a lonely place...