This will not affect you at all. They're not stopping allowing you to transfer books to your kindle over USB. They're stopping letting you download book files from Amazon.
In order to download and transfer Kindle books from the Library, I have to first add them to "My Content" on Amazon, then from the Amazon interface click "Download & Transfer via USB". That's the only way to access the AZW3 files that get moved over to the Kindle.
Either I'm missing something more obvious or the system I've seen libraries use for digital books over the past 10 years is more uncommon than I realized.