Outlook seems to keep everything in one giant file - damage that in any way and your contacts list, your mail records, and everything else disappears. Back it up every day!
Thunderbird, if left to its own devices, buries its mail folders deep deep deep in your C-drive. It does, however, use lots of separate mail folders so a glitch in one doesn't goof up the rest.
It is possible, relatively easily (like under 15 minutes if all goes smoothly) to move your mail folder to somewhere you can find it and back it up automatically. Mine's in the imaginative location called I: \Mail - "I" is my Internet Stuff drive.
If you do that, it's a good idea to edit the master mail control file - called Profiles.ini - so that it points at the new location. Then, if you create new mail accounts it will put them in the right place.
It's also not very imaginative in what it calls the mail folders, but those too you can change to something more meaningful - you just have to tell it what they are.