I remember at one point Mag asking whether this should have an incognito bonus, and Kinak said that it's working as intended.
Anyway, it does seem to have some hidden Incognito when scanning for files - on a Level 1 Blog:
- With no scans: Public files = +7 alert
- With quick, file, and deep scans: Public files = +4 alert
- With quick scan: Public files = +4 alert
- With file scan: Public files = +7 alert
- With deep file scan: Public files = +7 alert
- With network scan: Public files = +7 alert
EDIT: Added more to the above list. Looks like the quick scan is the only one that matters. See Joseph Phillips's Live Ideas for details.