Thunderbolt Display's audio 'cracking, hissing' noises after El Capitan upgrade
I have the same issue since El Capitan upgrade (2012 MBA).  No other TB devices connected apart from the display.  A restart seems to help, for a short time, as does switching the audio output from the display to the internal speakers and back again.

Removing all USB peripherals plugged into the display seems to prevent it happening, but is not exactly a "solution".  Other devices are just a Apple USB keyboard, Logitech wired mouse, and a powered USB3 external HDD.

I thought it might be a grounding problem (no idea why the OS upgrade would affect this), but no amount of grounding the aluminum keyboard to the computer casing, or the display casing etc. seems to make a difference.

I am not aware of any core audio plugins installed - any way to find this out?