Whenever trying to use pcsc-shared with nk3 the most prominent issue is that after running any operation that requires the pin and waiting about 30 seconds the card throws:
gpg: public key decryption failed: Bad PIN
whenever trying to run any operation.
The only solution when that happens is to kill scdaemon, preferably after any operation involving the nitrokey. Alternatively re-plugging the nitrokey works too.
This was already reported as Nitrokey3 SSH (via gpg-agent) stops workin after ~3 minutes - #2 by Koren23 but the workaround only works for ccid-enabled gnupg builds. As some distros actually ship with ccid support disabled in gnupg this is not a real solution.
As this allegedly works with yubikey, I wonder if the firmware could do something differently here to improve compatibility.