Parallel access of applications to Nitrokey (and to smart cards in general) is troublesome. As a best practice, between GnuPG, OpenSC and Nitrokey App, exit the applications which you don’t use at the moment.
To be honest: I think “Exit” is not enough: I was not running GnuPG in parallel. I assume the driver for OpenSC “grabbed” the device and so GnuPG was no longer able to get access. Only after removing the OpenSC installation I was able to use GnuPG again.
Now saying that , GnuPG has also announced, that they have some trouble with mail under macOS Sierra. So maybe this will be solved by them in the future.