"All My Files" Folder was Emptied when I Deleted Content of the Downloads Folder
The "All My Files" folder is actually a virtual folder, using Spotlight to find all the documents, pictures and videos which you may have and displaying it to you in a categorized manner.

Deleting the contents of "Downloads" will potentially remove some documents you may find listed in "All My Files" (if they were located inside Downloads), but does in no way remove every single personal file of your computer.

On the other side, if you inadvertently opened "All My Files" thinking it was "Downloads" and removed all files there, everything what Spotlight can find will be placed into the Trash.  Since "All My Files" gets opened by default when opening a new Finder window, it is a possibility.  This behavior can be set inside the preferences of Finder.

Additionally you stated that you preferred "console", which I interpret as using Terminal or command line (Console is actually an application which allows you to see log file output) over GUI, which is very powerful and can easily lead to dataloss when forgetting to type certain characters, especially when using "sudo".

Example would be rm /Library/* vs. rm ~/Library/*.  The first would go for the system-wide Library folder while the second would use the Library folder of the currently used user.  Removing all the contents of the Library folder, user or system-wide, is a bad example, however, both folders do exist and just one character can have a profound difference.

Finally, when one (or more) of your files where so-called application or package bundles, it is normal that you delete one file and Trash when emptying shows the number of each of the bundle files.  This would not explain "All My Files" being empty thereafter, but depicts the difference in putting a file (bundle) into Trash vs. emptying Trash.