There are two reasons for this. The first reason is that Link Whisper can’t show the correct number of links in the Links Report without scanning all the posts that will be shown in the report. It needs this scan to find the links and determine if they are inbound or outbound internal links.
The other reason is that Link Whisper uses data from the link scan when making suggestions. Link Whisper uses the link scan data to see if the current post already links to a suggested post. If the post has a link to the suggested post, then the suggestion is removed from the list.