When $wgUploadMaintenance is set to true, it should prevent any modifications from the upload repository: uploads (and reuploads), deletions, file renames.
Upon deletion it correctly displays an error stating the repo is in maintenance mode. However, the upload form doesn't give any warning, and uploading a file actually succeeds.
https://www.mediawiki.org/wiki/Manual:$wgUploadMaintenance
Reproduced on MediaWiki 1.30