I'd never remove the complete EGR system on a 6.7. The cooler isn't problematic (like the 6.4 coolers), so other than reducing a little weight and cleaning up the engine compartment, I see no real need. Plus, if you ever plan to return the truck to "stock" for warranty work or before trading it off, it takes 6+ hours to remove it and I'm sure twice as long to reinstall it, since you won't be able to find all the parts and if you do, you won't be able to remember where they all went.
You need to install a set of EGR block-off plates, which is a simple procedure (about 10 minutes). If you don't, the EGR valve will still be exposed to the soot from the motor and will eventually lock-down, which may or may not be covered by warranty.