kzmaier
I think your right Brundlefly.  A silent audio sample is a unit of data.  Perhaps in compressed audio the silence is not a factor in file size (mp3).
 
CJ - I would still like my saved projects to contain only relevant data for transfer and archive.

ZIP was developed primarily for text type data, where the common occurrence of similar strings of data (how many 'the's' are in the file?) allow for pretty impressive compression. It can be used for other forms of data, but the more random the data is, the less compression you can expect. The main savings in MP3 is the deliberate loss of audio data that is expected on the basis of psychoacoustic factors to make the final sound less easy to distinguish from the original. FLAC is lossless, and optimized to compress the kind of data in an audio file, but it can only be applied to pure audio, not mixed forms of data like a Cakewalk project. Most forms of compression will find a long string of zeroes easy enough to reduce in size dramatically, so true silence (absence of data) will compress only a bit more than audible silence (minutes worth of bytes representing zero). 

i'm just doing this in a cross-country collab, and finding out that the new Sonar Platinum isn't making proper .bun files, is "forgetting" to include some .wav's, and won't even open bundles it JUST saved.
 
anyone else experience this?

gbowling
Before you upload, create a new directory and save the entire project in this new folder. It will only save what's currently used in the file so it effectively "cleans up" your folder. 
 
If you do that and go look at the size of the old dir vs the new dir, you'll see that the new one is much smaller. 
 
Then you can zip/rar if you like. 

I would definitely go by the "Save As" to clean up recommendation. This is the best you can do quickly to eliminate audio files which are no longer needed. Then zip and upload ...
 
I would not bother with anything else (especially not manual changes like stripping silent sections) because (a) it takes precious time which you can spend elsewhere and (b) your project may not sound the same afterwards because you might have edited something just a little bit too much (the human factor comes into play)