From what I can tell, they are stored in
I have a lot of apks in that directory. I downloaded the one from today and I now have a new file in there dated today with the time stamp of when I purchased the application.
The files in there seem to use some "identifier" that amazon uses for the application. Cleaning out this does not affect the amazon app store in any way, but if you want to install an application that you previously purchased, you will have to redownload it, which it does with out any issue. I just cleared my directory out and tested this.