When inserting a reference to image on a page (e.g. [[File:Image.png]]) that does not exist, MediaWiki will in general (if uploads are enabled) create a link to where you may upload an image with that very name.
However, should you be using a pool wiki (for the purpose of keeping your images centralised), this link will still refer to your local Special:Upload, and if you disable uploading on your local wiki, for the sake of avoiding people uploading there and refer them to your pool wiki, the link won't work at all.
MediaWiki needs a better way of checking this. And using $wgUploadNavigationUrl seems awfully close to a "hack", a better solution would have been a basis, so rather than creating a link to say, "http://pool.wiki.tld/wiki/Special:Upload", it should rather have contained "http://pool.wiki.tld/w/index.php".
If people using "http://pool.wiki.tld/w/index.php?title=Special:Upload" rather than its prettier version is a concern to you, perhaps write something even better!
In any case, the current version lacks a version for inserting queries (unless you want to simply append them to current link, but MediaWiki doesn't seem to approve of that internally, eh).