As already stated, a hacked console with B9S will remain hacked, no matter the firmware version.
I however suggest you not to update Luma automatically (updating it is as simple as replacing one single file on your SD card) and not to update to the latest system firmware immediately, but only after visiting the forums and checking any compatibility issues.
In this case, version 11.6.0-39E was released a couple of weeks ago, but a new firmware version may turn some homebrew applications unusable, and there is usually no compelling reason to update (other than being able to play the latest game, if at all.)
Updating Luma (and its payloads, like GodMode9) manually every now and then forces one to review their setup, read the new features and check for any issues.
Administering and using a system are two completely different tasks. Do not mix them.