Manual:$wgUseCommaCount

Details
Under which condition should a page in the main namespace be counted as a valid article? If $wgUseCommaCount is set to true, it will be counted if it contains at least one comma. If it is set to false (default), it will only be counted if it contains at least one wiki link.

Retroactively changing this variable will not affect the existing count. There is currently no maintenance script to fix up counts. initStats.php will update good articles to be somewhat close to what it should be if this variable is set to false (It counts outbound page links, where presence of [[ is whats really counted).