What is the best way to delete discovered devices from zigbee2mqtt?
Can I just delete them manually from configuration.yaml, database.db and state.json or is there a better more correct way?
When searching it seems there are several ways.
Yes, that will work. But Zigbee2MqttAssistant has a feature for removing devices from z2m network.
Didn´t even know there was a web gui. I will try it out 
Is it only availbale for Hass.io and not for Hassbian?
You can install Docker on Hassbian (it’s just Raspbian under the hood).
Okay but would that be an advantage compared to just installing Docker on the Rasbian Stretch Lite where Zigbee2mqtt is installed?
Has someone tried to install it from Docker on a Synology NAS and knows where and how to make the appropriate settings?