On my Debian-systems, the timeframe for the detection of/working with NK3 on Debian is short.
It seems that -after a few minutes- the system just doesn’t recognize the NK3(mini) anymore.
Same with KeepassXC: I have to re-insert the NK3 everytime shortly after I (re)start Keepass, otherwise it doesn’t work.
Is it a Debian-problem, or an App-problem or has something to do something with Gnupg?
That does read like your system auto-suspends the USB ports, such behaviour can be configured. If you’re not used to it, powertop is a tool you can use to look at it.
Instead of re-plugging, you can also issue nitropy nk3 reboot.
I can confirm that i use a Debian 12 laptop with an NK3(mini) permanently in the usb port and i’ve never had any issues so it might just be isolated to you.