One of the best ways to keep Max for Live devices sorted would be to import those directly into your User Library of Ableton Live. You could just drag and drop the .amxd file (=file format of M4L devices) into your “File Browser” of Ableton Live.
You could as well store M4L devices in a folder anywhere on your computer.
Important: When you use a M4L device in an Ableton Live set it will be ‘grabbed’ from the folder where you stored it – so it is not included per default in your Ableton Live set! This is the same for external samples, presets and so on. As soon as you move those files the file-path on your computer changes and won’t be found by Ableton Live per default.
This is why I advice you to store external files in your User Library directly.
Of course back-ups of your files and OS should be happening on a regular basis as well!