I had the same problem with a new 3321.
I harvested the PCB from an old 3320 and stuck it in the 3321 chassis with the 3321 reader/faceplate sure enough all the tags that would not work before suddenly worked.
This confirms the reader itself supports NTAGs just fine even on newer models. It is the mainboard PCB on the door side or firmware on it for sure.
I can’t confirm firmware versions and the chips are covered in epoxy which is a pain… however comparing the boards side by side I noticed they are identical with one exception: the old one has two pairs of diodes populated and the new one leaves them unpopulated.
I am wondering if this is not firmware at all, but someone cutting corners and someone in QA only checking it still worked with the samsung mifare classics and not bothering to test anything else.
It will be a couple months before I am done moving in and can setup my EE lab again, but if anyone with a non working unit laying around wants to populate those 4 pads with diodes it would be worth trying.
Else I’ll get to it myself and report back eventually. Just figured I would share my terrible workaround and the potential implications