The picture you are showing is the default status for the Department and Site Quick Keys. There are similar windows for Favorites List Quick Keys (in the Profile) and for System Quick Keys.
This sets the initial/default status of the given Quick Key. Checked means the Quick Key is On, unchecked means the Quick Key is Off.
I need to point out you use the words "System Quick Keys" but you are showing Department/Site Quick Keys in the picture. System Quick Keys are different from Department Quick Keys.
I suspect you might be used to older model scanners where sites were associated with System Quick Keys. That changed in the x36 line of scanners, where sites are now at the Department Level. (There used to be 2 levels/layers of Quick Keys, now there are 3). So that might be what's throwing you off.
On default status, it remains that way until you do something to change it, such as turning Off a Quick Key that was On by default (pressing FF.SS.00 Eyes) for that Department 00 Quick Key.
If you turn off all System Quick Keys, you'll probably see "Nothing to Scan". The only way you would not see that is because there is an active System being scanned that does not have a Quick Key assigned.
To "undo" all System Quick Keys being turned Off, just turn them back on. Let's say you have System Quick Key 0 in Favorites List 1 (and it was on by default). You press 1.0 Eyes to turn it Off. Pressing 1.0 Eyes again turns the System Quick Key On.
A similar process for Department Quick Keys, but you add that third layer for Department/Site. Using the example from above, with Department Quick Key, the process is pressing 1.0.0 Eyes to turn it Off, and 1.0.0 Eyes turns it back On.