Because you have 2 hard drives, not 1.
 
If the chance of 1 failing is 1%................................

I guess for me this goes way back to the days of working in an administrative office. I was the "boy" and one of my jobs was filing stuff. That was the railway but I'll use a Dentist office as example. 
 
A computers "file" system can be thought of just like a real filing system. 
A Hard drive is the Cabinet and there are drawers and folders. 
In a dentist office you would never put the patient files in a seperate cabinet or drawer. 
Everything to do with that patient would always be in their folder. 
 
And because most everyone uses a second Data drive which these days can hold a lifetimes worth of project files, it's not something one should have to worry or fuss about "making room" or worrying about size of projects anymore. 
My Data drive is for DAW storage only so the folders are at the top of the tree. In otherwords all the drawers are visable when you open this drive. 
Each Drawer is for storing the different things and a drawer for each sub catagory of Sonar projects. I always add the date so when I drag and drop to other drivees it is clear how up to date the back up is. Rough example: 
1: Backing Tracks July 5 2015
2: Client Joe April 2 2015
3: Client Mary Jan 2015
4: Originals Apr 2014
5: Song Ideas
6: Original Masters
7: Original MP3
8: Joes Masters and MP3
9: Marys Masters and MP3
 
Inside Client Joe's folder you will find a folder for each of his Songs. In each of those folders is the following:
Audio folder
Mix Scenes folder ( new) 
CWP  file
MIDI   file
Lyrics Doc
MP3 of covers version or rough recording if original. 
 
After a session with Joe, I drag and drop the whole Client Joe folder to my 3rd data drive and give it the new date. There will be a couple of the same Client Joe folders with older dates too. I don't toss anything out until Joe is a done deal. 
Every once in a while I will also copy the latest Client Joe folder to an external drive. That drive goes with me and those files are also then copied to another computer 300 miles away. 
 
So anyway's using your method would be a mess for me because it would meen double the work. 

Cactus Music
 
...In each of those folders is the following:
Audio folder
Mix Scenes folder ( new) 
CWP  file
MIDI   file
Lyrics Doc
MP3 of covers version or rough recording if original.

 
I often create a another sub-folder to store plugins' settings that I have used within the project. Some people might prefer to store them in each plugin's own folders, but that entails to risk of them getting overwritten or deleted when you update or reinstall the software. Many plugins don't seem to have an obvious place for saving settings anyway. Whenever I want to re-use some (non-default) fx or softsynth setting that I previously used in a particular project, I know where to find it.

I never though of that one, good tip. 
You just gave me an idea about custom samples. 
Client Joe wanted a railroad spike for his version of 16 Tons. So we made our our sample and stored  it in the Session drummer folder.  I built a new DAW and that sound was missing so I had to fire up the old DAW to dig it out. 
I should keep a copy of that sample with that song. 

Cactus Music
...we made our our sample and stored  it in the Session drummer folder.  I built a new DAW and that sound was missing so I had to fire up the old DAW to dig it out. 
I should keep a copy of that sample with that song.

 
If you used an audio sample in a project, there will be a copy of it in the project's Audio folder.

If I ever make any samples or sfz files for future use, I keep them with the DimPro multisamples or Battery kits, which are on a separate drive.

I do a couple things with any custom synth presets I may create for a given project:
 
1.  I save any custom synth or effects preset with the project name as part of the preset name, as it is particular to that project, and it is saved to a Presets folder that I create, if needed, within the Project folder, so that this preset will always be able to be found, as long as the Project folder exists.
 
2.  If I think the custom preset may be usable for other projects in general, I may also save it to the normal folder most synths/effects have for User Presets.  This makes it safe for another project to tweak it with no danger of accidentally destructively altering a preset needed for the original project it was created for.
 
I also am wondering why you would choose to go through the work to create these Audio folders within the global audio folder, or wherever it is, rather than keeping the audio within the default Audio folder that is created within each project's folder in Cakewalk Projects.  A 2 TB drive is less than $100 these days, and has plenty of room for storing backup folders of all of the projects, and just following the defaults - backups are as easy as copying each project folder to the backup drive, etc...
 
Bob Bone
 

robert_e_bone
I also am wondering why you would choose to go through the work to create these Audio folders within the global audio folder, or wherever it is, rather than keeping the audio within the default Audio folder that is created within each project's folder in Cakewalk Projects.

 
Bob,
My main reason for mulling over the idea was that this:

...seemed more distinguishable and attractive than this:

 
Notice in the second example (using the default per-project destinations) how the "Audio", "Audio Data", and "Picture Cache" folders are all mixed up amongst the project folders, rather than clearly separated and discernible like in the first example (my proposed method).
 
But again, one thing I hadn't considered was auto-save and versioning copies of the all of the .cwp files, which would make my example not so pretty anymore. So, given that (along with other good reasons that folks here have mentioned), I've conceded that it would be wise to just go along with the typical per-project functionality, and maybe get around my aforementioned qualm^ by just saving all project folders into a "Projects" subfolder of sorts within "Cakewalk Projects".
 
 
PS: Don't mind the project names in the pictures. They're just blank dummy files given random song names for this discussion. No copyright infringement here!
 
 

You CAN move Picture Cache and Global Audio Folder to a different location, by the way.  You can give them each a new location in Preferences>File>Audio Data.  Just go here, and specify a new location for either or both.  I chose to put them both under Cakewalk Content, but it is entirely up to you.
 
Maybe that would have you feeling better when you look through the Cakewalk Projects folder.
 
Bob Bone
 

robert_e_bone
You CAN move Picture Cache and Global Audio Folder to a different location, by the way.  You can give them each a new location in Preferences>File>Audio Data.  Just go here, and specify a new location for either or both.  I chose to put them both under Cakewalk Content, but it is entirely up to you.
 
Maybe that would have you feeling better when you look through the Cakewalk Projects folder.
 
Bob Bone

 
What about the default "Audio" folder (the one that's used if you're not using per-project folders)? Can that be moved, deleted, or hidden without causing any problems?