If you have the regular 9.00 jailbreak USB plugged into your PS4 when you are booting your PS4 it will not cause any permenant damage but it can cause problems.
It might say something like "there is a problem with the PS4" and not boot.
To fix this just make sure you remove the USB, shutdown and restart the PS4 and all should then be OK.
Or, worst case scenario (This happend to me once).
It will not boot, even when the USB in not inserted.
To fix this just boot into safe mode and select "Restore default settings".
This should be enough to make the PS4 boot again without having to reinstall the system software or anything like that.