By unchecking the DLL’s you won’t gain that much time wise.
The best way to cut scan times is by using the persistent cache.
Another way is to uncheck the “follow links” during scans.
Instead use the “scan in order stored on disk” option.

As far as the risk factor anytime you fail to scan “any” executable you run the risk
of something really bad happening.

edit: Anytime after you run a scan and access an executable it will be scanned again.
Not just by the file shield but since it will no longer be in the persistent cache it will be scanned again
the next time you run a “regular” scan.