$wgUploadNavigationUrl should be used for file redlinks if $wgUploadMissingFileUrl is not set. The first was used for this until the second was introduced in r69997 (1.17). According to the comments there it was broken in 1.16 but as far as I tested it worked in 1.16. In any case, the old behavior should be restored as most WMF wikis have set wgUploadNavigationUrl but not wgUploadMissingFileUrl.