Computer does not boot after EFI partition format

Feb 1, 2015
Intel NUC D34010WYK
Intel HD4400
MacBook Pro
I have an Intel NUC, model D34010WYK with a mSata SSD.
I had El Capitan up and running together with a Windows partition.
I no longer had use for Windows and also had to reclaim space for the macOS system so I deleted the Windows partition together with the boot entries in the EFI partition.

After that, the system would not boot anymore (no bootable device found) so I looked around for a way to reformat the EFI partition and reinstall Clover in it. I found this Terminal command:
newfs_msdos -v EFI /dev/disk0s1

I then reinstalled Clover and rebooted the system.

My system now is frozen on the Intel Splash screen and I couldn’t enter Bios (F2) or boot the system.
I flashed the BIOS with the most recent version (0045 as I write this) and reset it, to no avail.
I removed the mSata SSD and booted with just a USB installer of Sierra. With this I was able to enter the BIOS and boot from the USB.
When I reconnect the SSD it freezes again.

So, the SSD is freezing the computer, probably because the system can’t recognize the boot partition anymore.
I can’t even connect the SSD elsewhere to test because it’s a mSata interface, it only fits in the NUC.
I don’t know what else to try, any input is greatly appreciated.