today i found a way to fix the problem when Logic Pro crashes/hangs while scanning the Audio Units.
This is going to be a little complicated.
On OS X 10.11 El Capitan, Apple implemented the new version of Audio Unit (3), many plugins do not pass the validation.
To validate them Logic uses a programm called auvaltool. You can replace it with an older version (which can be found online) and everything works fine after rescanning.
Before you can replace the auvaltool you have too disable the new “System Integrity Protection”, which is one of the new el capitan features and protects system files from beeing modified (like the auvaltool).

1. Disable System Inegrity Protection by rebooting into recovery partition. Then open Utilities-> Terminal (Shell comand window)
type in “csrutil disable”, without the “” and press enter
to restart your mac type in “reboot” and press enter

2. Download old version of auvaltool, for example from here: https://discussions.apple.com/thread/4081659?tstart=0 or try this one here.

3. Open Finder, click on Go To -> Got to folder and type in “/usr/bin” (without the “”)

4. Search for the file auvaltool and make a copy of it to your desktop (if something wents wrong)

5. replace auvaltool in the /usr/bin folder with the one you downloaded in step 2

6. Restart Logic, Open empty project, Go to Settings-> Plugin-Manager. Select not validated plugins ant click on rescan

Thanks to matthiaswitt over at the NI Forums for the tip.