Good news everyone! Native Instruments can work with the newest OS X. Lets hope Pro Tools follows suit soon with 11.
Please note that the compatibility issues connected with Mac OS X 10.11 El Capitan are now resolved.
The latest OS X 10.11.1 update fixes the issue where Native Instruments Audio Units plug-ins did not pass the AU validation and therefore were not available in Logic Pro X.
New drivers are also available that fix the issues experienced by users of MASCHINE (MK1), RIG KONTROL 3, and older TRAKTOR hardware.
For more information, please read this Knowledge Base article.