Luckily, there is one simple possibility: SharePoint Designer allows you to hide lists/libraries from the “All Content” view. Any items that are hidden from this view are also hidden on the mobile view. This setting does not change permissions, so the list/library will still be available on the site. Users will still be able to navigate to it if they know the URL, it just doesn’t show up anywhere in the nav. This would have to be done for each list/library on each site, but a PowerShell script could be created to automate this for particular libraries, if desired. This certainly isn’t a perfect solution, as the power users who need access to these libraries will now be inconvenienced and will need to either have bookmarks for these libraries or open them via SharePoint Designer.
1. Using SPD, open the desired site
2. Click on “lists and libraries” on the left side
3. Click on the name of the offending library
4. check the box for “Hide from Browser”