Ignore previous update. The lack of an AT_SIGNATURE key type is normal, and should not be a problem. It’s possible SignTool is insisting on an AT_SIGNATURE key, but if so that’s a bug in SignTool.
Looking at the source for the OpenSC minidriver, it appears it will return the key as AT_SIGNATURE if the private key usage is suitably constrained. I’ll experiment.
I’ve just confirmed that Microsoft’s VsixSignTool utility works correctly with the NitroKey HSM (via CAPI), prompting for the PIN. So the problem so far is limited to SignTool. If I figure out what’s going on there I’ll post a followup, but it doesn’t look like a NitroKey or OpenSC issue.