I'm so grateful I found this post and thread -- in my case, because with El Capitan my Intellitype Keyboard 4000 has also lost all its HotKeys...now I understand why, because I assume it's the same driver issue for the keyboard:
"Intellitype software doesn't work on El Capitan because of the System Integration Protection feature.
I disabled rootless through the recovery partition using the csrutil command in the Terminal window. Only then I was able to run Intellitype and Intellimouse apps.
Apple strongly recommends to leave rootless enabled."
I'm not going to disable SIP to get those hotkeys back, and I'll keep using my Intellitype because it's the most comfortable, ergonomic keyboard I've ever used, but I sure hope that MS does a quick fix on this. I miss how fast I could do things with the press of a key with those Hotkeys!