No, I know what you’re saying. Out of the box, Mint will not log that swf files access. The reason is what you stated, accessing swf files bypasses the Javascript used for tracking. Size doesn’t matter, etc.
awstats uses server logs to analyze site usage. Mint uses Javascript to track and therefore does not catch every little thing on your website (its goal is to eliminate useless junk, but in this case it matters to you).
There was a Pepper out there for Mint 1 which may work in Mint 2. The Pepper analyzed downloads via server logs. That may work for you for tracking swfs, but I doubt it since an embed usually does not count as a download. There was also a flash tracking Pepper for Mint 1, but the reports seem to indicate it does not work in Mint 2.
If your sole goal is to eliminate CPU usage on a high performance site, Mint isn’t going to solve that. I’d wait for Shaun (Mint author) to back me up on this, but writing apache logs would take significantly less processing power compared to the php processing and database connections needed to process a Mint hit. However, keep in mind that with proper configuration, you could run Mint from a separate server.
So yeah, it doesn’t seem like Mint will do exactly what you’re looking for. Really the only thing which will do what you’re looking for is apache logs and some program such as awstats that analyzes the logs. Any other service such as Google Analytics would miss the flash tracking as well.