I have recently had an issue with Indesign CS6, everything seems to run fine apart from the toolbars, when you click on 'Layers' for example it takes an age to pop out. I have been using CS6 with El Capitan for a while now with no problems. I have tried resetting the preferences and reinstalling but nothing has helped so far.
CS6 is now almost four years old. Other have experience slowness problems with CS6 in El Capitan. There will be no updates to CS6.
The only answer I know of is to switch to Creative Cloud and/or get a faster computer.
I had this problem and I eliminated it by turning off Growl and restarting my Mac. Good luck