Here are instructions on how to reinstall usb fax modem support on Mac OS Sierra: Reinstall USB Fax Modem Capabilities on Sierra. It simply involves copying a few files from a previous El Capitan install. It works on my system, and the working fix is persistent after the 10.12.3 upgrade.
I filed a bug report and was told that Sierra supports multi-function printer faxing, but not "legacy" fax modems.
Personally, I have no interest in adding more peripheral clutter when all I need is a sub-$15 modem and a phone cord, especially when the fix is copying over a few files.
If dropping support for fax modems affects you negatively, please take the time to issue feedback at Apple's website, https://www.apple.com/feedback/macosx.html.