When looking at the top sites reporter in Reporter we only see some of the HTTPS that users are accessing.
When protocol detect is set to none in policy we will only log protocol scheme tcp:// since we don't see HTML content, the page view and browse times will remain at zero, consequently these sites will not show up in the top sites report.
Customer is uploading both the main access log and the SSL access log to Reporter.
Customer has policy to disable detect protocol for some sites.
If protocol detection can not be enabled for these sites you will need to create a report based on total bytes received, while not the same as a top sites report, it will at least include the data for the missing sites.