Sorry for the delay in my reply, I didn't get a notification for your post... weird..
Currently:
If pause index updates is enabled on startup, the USN Journal monitors are not started.
If the monitors are already started, pausing index updates them will keep them running.
Changes will be detected, but your index will not be updated until you unpause or exit Everything.
This could be undesirable if you expect Everything to not make any changes to the index on exit while the index is paused.
The next alpha update will stop the USN Journal monitors and process any pending changes to the index when pausing updates.
Folder monitors will continue to watch for changes (even when paused), otherwise Everything could become out-of-date.
Changes to your folder indexes are not made until you unpause or exit Everything.
I don't think many people will have a serious need to halt the monitors in 1.5. Especially since index updates are non-blocking now.
The reason I did pause the monitors has an entirely different reason: "noise-cancelling": to filter out irrelevant entries - for that specific case - in the debug view.
So not a big deal (to me) as most entries were relevant now. Just curious. As usual ...