My experience is from a school environment with 300,000+ endpoints
The pros and cons of running scheduled scans really needs to be weighed up in your own environment to really determine the value.
If your machines are turned on 24/7 and you can easily schedule an after hours scan then by all means run it!!
In most environments I find that you cannot guarantee that they will not impact end user's and hence I turn them off and rely on real time protection.
The only real benefit is when a user plugs in a new external USB drive that has never been scanned before.
I wish SEP had a setting that scanned new drives as they were connected although this would create its own issues as it would be slow on large drives.
Regardless of the scheduled scan the files are scanned by real time protection as they hit memory, or are modified or moved/copied from the external drive anyway.
If you have had an AV product installed every file on every machine has been scanned week in and week out.
Where is the value in scanning those same files again and again and again, slowing down end users machines.
It is a constant battle to keep end users happy with the product and the scheduled scan is probably the biggest culprit in creating a poor end user experience.
Although the scan at startup might be even worse :)
I run an active scan when new definitions arrive which checks the memory and common load points and is completed in a few minutes.
As drive indexing is enabled by default in windows, all of the files on a system will eventually be scanned as windows does its indexing whenever the computer is idle.
If you really do want to do scheduled scans then I would recommend choosing to not enable the feature that retry's the scan if its missed.
Eg. if a scheduled scan is missed at 12pm lunchtime on a wednesday and it is missed then it runs at 9am thursday when the end user turns their machine on.
This usually causes huge issues with end users trying to do presentations etc. or get on with their work.
Scheduled scans on servers makes sense as it is very easy to choose a time within a maintenance window after hours where the scan will not impact performance.
You just need to ensure that the scan does not interfere with backups or other maintenance tasks.