Not Multisite Ready

When files are uploaded, they are added to a single directory, regardless of which blog added them. Also regardless of date. This is of course extremely ugly and not compatible with the WordPress best practices (which would be to use the function wp_upload_dir() to determine the root of the upload directory). When there is a conflict, when a file is uploaded with the same name as a previously uploaded file, how the situation is handled depends on the blogs settings. If the blog setting is to replace the previous file, then the file is removed regardless of whether or not the file was from the same blog or another. That mean, one blog can remove files from another blog.

Not good.

Why is wp_upload_dir() not used?

That’s exactly the point: it loads everything into the same directory, regardless of the blog. On a multisite, that means that one blog can replace the file used by another blog. It seems to me you must put each blogs uploads into a separate directory.