Here is the solution I came up with. Not sure it is the best way or simplest, but it works so far. Feel free to critique or improve please.
set key="HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Print\Printers"
reg query %key% > temp.txt
FOR /F "delims=" %%a IN ('findstr /B "HKEY_LOCAL_MACHINE" temp.txt') DO (
if /I NOT "%%a" == %key% (
reg add "%%a\PrinterDriverData" /f /t REG_DWORD /v SSNPNotifyEventSetting /d 0
)
)
First, I query the registry and save all the needed reg keys into a text file. Then, inside the FOR loop, I search the file for the different registry keys and add the new sub key if not in he root key. I've added this to the tool I'm building to fix print servers and it has been great so far.