Lock LUKS with Nitrokey on Fedora/QubesOS

The crypttab is not used for the system’s root partition, the root device is specified via kernel parameters (e.g. rd.luks). Have a look what parameters you have set and compare to the devices.

While there are different naming methods, not all will work to boot. To get started, identifying the correct device via /dev/sdaX should definetely work. This only gets problematic, when you have multiple devices on the system.

The emergency shell cannot be regenerated from the initramfs. For that the system should be fully booted, because dracut needs to access the configuration files etc
What you perform in the emergency shell is to unlock the LUKS cryptdevice and perform the steps to mount the system root. Next, upon exiting the recovery (‘exit’) it should try again to boot.
If you have trouble performing the steps in the recovery shell, you can perhaps boot a USB-live system to unlock the LUKS device and inspect parameters. You can’t regenrate the initramfs then directly either, but must first chroot into the borked system to let it regenerate the initramfs. Still, it may be easier to look what’s wrong via a live system.
HTH