Well, I get the same.
On 10.11.4 with OsxAptioFix2Drv, it occasionally boots to the prohibited sign, same as ever. If you don't mind Ctrl-Alt-Del when that happens, fine.
On 10.11.4 with OsxAptioFixDrv and CsrActiveConfig 0x3, the NUC doesn't boot (if you wait long enough, you still get a prohibited sign).
On 10.11.4 with OsxAptioFixDrv and CsrActiveConfig 0x67, it works fine.
So I guess the advice is, fire up Clover Configurator and on the RtVariables screen change CsrActiveConfig from 0x3 to 0x67 before updating to 10.11.4.
If it's too late and your NUC won't boot, you can boot to a vanilla UniBeast USB drive (10.11.4 is fine) using F10 to select UEFI:YourUSBDrive as the boot device, then select your regular OS X install from the Clover menu. This should get you in without graphics acceleration. But it's enough for you to run Clover Configurator and make the CsrActiveConfig change and save the file, and then you can reboot without the USB drive and you should be fine.