Recently saved a project in Cakewalk Platinum to a bundle to send to a friend.
 
It turns out that a click/pop artifact was introduced into one of the audio tracks, that is not present in the original (non-bundle) project. This seems to indicate that Sonar is processing the audio when it creates the bundle, instead of just copying the audio files over, which seems both unnecessary and dangerous, as it introduced a click/pop artifact on one of the audio tracks.

Could be possibly, although wonder why you would save it to a bundle?
If it's because it makes the project smaller, then i would guess that that's the answer to your question about it being somehow processed.

I was saving as a bundle instead of just zipping the project folder, because saving as a bundle only includes the audio actually referenced in the project. Let's say you bounce a VST synth 5 times, and delete 4 of the bounces. All 5 bounced audio files are still in the project's audio folder. Saving as a bundle would only include the bounced audio that was referenced in the project, and not the 4 that were deleted. I wouldn't expect it to process the audio from the one bounce that's in the project though. What would be the point of that?
 
The "clean audio" feature has never worked for me in the 10 years I've been using Sonar, seems to be a lot of posts supporting the fact that this is a broken feature.

I'm pretty sure if you use "save as" it only saves the audio used in the currant open version of the project.
So try save as and point the operation to the external storage your using.
I just collaborated online with another forum member and I stripped the project down and used "save as" for the new version. I paid attention to the file size and it most certainly became way smaller.
I used as much midi as possible as midi is real small. We all have the same VST's more or less.
The only Audio was Vox and Guitar.
I even turned my Bass part into midi, but I used the real bass in the final version.
The stripped down project is just used to send back and forth and when done you copy paste the new stuff that your friend recorded into the original full version.  
 
We used a Folder with the CWP and audio folder inside.

If you don'

David.Hoffman
I was saving as a bundle instead of just zipping the project folder, because saving as a bundle only includes the audio actually referenced in the project. Let's say you bounce a VST synth 5 times, and delete 4 of the bounces. All 5 bounced audio files are still in the project's audio folder. Saving as a bundle would only include the bounced audio that was referenced in the project, and not the 4 that were deleted. I wouldn't expect it to process the audio from the one bounce that's in the project though. What would be the point of that?
 
The "clean audio" feature has never worked for me in the 10 years I've been using Sonar, seems to be a lot of posts supporting the fact that this is a broken feature.

 
When you want to include only the the audio referenced in the projects, you have two options. Checking "Create One File Per Clip" in the save dialog saves only that audio that's present as a clip. There's another way to save projects that saves only the audio referenced by clips, but includes all of the file the clip references, without including files not referenced by clips. This is described in detail, along with other aspects of saving, in the tip "The Third Way to Back Up Projects" in The Big Book of SONAR Tips.

but the OP's question remains unanswered: "Save as Bundle... does it process audio, and why?"

Good question. Noel posted the bundle format a long time ago, and I thought it was uncompressed. Not sure if I remember correctly now.

I don't know, but I assume it doesn't do error-checking? Try saving as a bundle again and see if the same issue occurs. Perhaps there was some other computer process going on at the time that interfered with the packing process.

A lot of users have stopped using BUN files due to corruption and other issues. I use Per Project Folders and simply copy the entire folder when moving it to another system. There's a way to weed out the extra audio files not used in the project which keeps the folder as small as possible. I would not recommend any backup method that uses compression.
 
SONAR compacts all the audio and merges it with the remaining project data in a bundle file.
 
Here's a quote from Noel back in 2008:
 

Noel Brothwick
No, bundle files are not compressed in any way. A bundle file just contains what we refer to as "compacted audio chunks". All this means is that all audio at the same bit depth and interleave (stereo/mono) is packed into one chunk in the file. All clips in the project at the same bit depth and interleave are combined and written into a single chunk of data.
A bundle file is basically a multichunk RIFF file where each chunk represents a specific wave format. The actual SONAR project file is appended to the end of the bundle as the last chunk.

A typical bundle looks like this:

<64 bit float Stereo Audio Chunk>
<64 bit float Mono Audio Chunk>
<32 bit float Stereo Audio Chunk>
<32 bit float Mono Audio Chunk>
<24 bit Stereo Audio Chunk>
<24 bit Mono Audio Chunk>
<16 bit Stereo Audio Chunk>
<16 bit Mono Audio Chunk>
<CWP chunk>

Since a bundle is really a multichunk RIFF wave file you can even rename the file to a WAV file and actually play it or import it :-) Of course most software would only play the very first chunk in the file and ignore the others.
 

Mick
Bundles are indeed compressed.  I feel confident in saying this, as I just saved a project as a bundle, and while the total size of the project is roughly 70 megs, the saved bundle file is only 30.

Here's one of Noel's comments. There are many threads about bundles going corrupt. The audio data are not modified, but maybe the files are packed together in ways that may not be reliably unpacked.