I cant tell if this is an issue with El Capitan or Indesign or both - some panel menu fonts appear pixelated too, but this happens in other programs as well. Fonts in the layout in InDesign appear jagged - this is not happening in Word, for example. I'm using CS5 version 7.0.3, I think that's all the updates? Help! I'm going insane from this.
I'm afraid your copy of CS5 is end-of-life. There will be no more updates. The product will not properly install or run in El Capitan.
You'll either need to roll back to your old OS X version or get a subscription to InDesign CC 2015.
This actually sounds like a retina display issue. If that's the only issue you're having with El Capitan, consider yourself lucky.