Hi,
The link for it is on /Admin/AdminMenu.aspx it has never been on the site settings page.
In a multi site installation the default is to not allow child sites to use the File Manager since it provides direct access to the server file system.
If you want to have it available in child sites you could put this in user.config and set it to true
<add key="AllowFileManagerInChildSites" value="false" />
I have it disabled on the demo.mojoportal.com site for this reason, I can't allow strangers access to the file system.
Hope it helps,
Joe