Good knife shops with a selection of high quality folding knives are really rare in Germany IMO. You will find cheap hunting knives, SAKs and kitchen knives in a lot of shops (kiosks, super markets, cutlery shops, tool shops etc) but high quality folding knives are rather rare.
I recommend you to go to Solingen if possible. Its only 60kilometers from Bonn and can be reached by train or car within 40-60 minutes. Solingen is/was the knife capital of Germany. Nearly all major brands and most importers still have their offices and part of their production there. Most of them have shops. For a knife nut in Germany it is worth the trip!
In Solingen Böker should be worth a visit (
https://www.boker.de/en/knife-shop). They usually have good deals on knives from their own brand and also sell imported knives. But there others like Puma (
https://www.pumaknives.de/en/about-puma/factory-sales/), Eickhorn, Hubertus and Klaas (
https://klaas-messer.de/i/werksverkauf). Most German kitchen knife and cutlery manufacturers also have a factory sale in Solingen.
If you have a time you could also call / write to Otter (
https://www.otter-messer.de/de/). In the past they sometimes offered people to visit their production of traditional knives.
Regarding shops from Bonn or Berlin: Nothing in Bonn. Messerworld (
https://www.messerworld.de/) has a shop in Berlin. They seem to have a selection of nice knives.
If you like tactical knives you could also write to SARTOOLs (
https://sartools.shop). SARTOOLs it the online shop of a firefighter, knifedesigner and knife modder from Berlin. He is importer of many American an Italian brands and even though he has no walk in shop he might allow you to look at a knife in person if you contact him in advance and arrange an appointment.