For anyone facing issues with the keyboard input not working in the firmware updater, it is a driver issue in syslinux (the mini-OS that the firmware updater uses). It fails to initialise the USB ports - there may be a fix for that, but the easier workaround for me was to use a USB to PS2 converter with my keyboard. Using the converter, I was able to go through the update process without any issues with both of my EVO Plus NVMe drives installed in the M.2 sockets. If you have multiple NVMe drives connected, the updater goes through them successively, asking the Y/N questions about each of them separately and identifying them by their serial numbers, so you don't need to worry about unplugging one to update the other. Also, updating the firmware did not break the Windows installation I already had on one of my drives, even though the updater warned me of the possibility.
EDIT: Just to note that updating the firmware fixed the kernel panics during installation on my build, and I can highly recommend the EVO Plus NVMe drives now that there is an easy fix available. I now have a working Hackintosh build thanks to the firmware update.