Not really. It means, in addition to other times that scans are invoked (like when newly deployed updates are received), run the scan. The scheduled scan cycles as supplemental to process of deploying updates and not in the critical path for them.
what if i deploy something at 9:00 AM, will it wait for the next day 3:00 AM?
No. As noted, update deployments don't specifically rely on the scheduled scan cycles. Thus, I generally recommend folks leave the default values for the scheduled scan cycles.
Here's an older post I did that has a handful of notes that may be helpful: https://home.memftw.com/notes-software-update-scan-cycle/