The notification means:
In order to refresh what the Triggered Sends might have to respect newly, or no longer respect - your new auto suppression configuration - the system will:
- 1 pause
- 2 apply changes
- 3 "Publish changes"
- 4 Restart
all triggered sends.
Every message request that trickles into your TS between 1 and 4 will stay in the queue during that "paused" time. The notification tells you that it will go through the queue after 4 so that no messages are stuck because of the change.
I showed the manual steps above for clarity's sake, but the system does all of that automatically in this usecase.
As you say, also journeys are based on the same infrastructure.
Since you do not have to do anything manually with normal TS, it would also be plausible that you have to do nothing in your journeys. I cannot give you a guarantee, but why I think it's plausible is because even the manual steps are simplified in journeys. Instead of 1-4, you really just have to edit the email and hit save, JB streamlines steps 1-4 for you (but you still HAVE to do it to apply changes!).
So it would be really odd that in this particular case with Autosuppressions, where the system automates the whole thing for us, the already simplified Journeys would be left on the wayside.