Custom recovery and Google OTA Will I receive Google updates for my Galaxy Nexus if I replace stock recovery with CWM (like explained in Why isn't Clockworkmod Recovery “Sticking”)?
Having CWM installed won't prevent your phone from noticing that an update is available, but it may prevent the update from installing in the usual automated fashion.  The update process actually works by creating a special file with a "script" for the recovery to run, then rebooting to recovery; CWM will just show its menu instead of running the script.  It may be possible to apply the upgrade through CWM as an ordinary update zip, but if you want to make sure the process is seamless, it'd be a good idea to flash back to the stock recovery before installing the update.

BTW, the JRO03O update for the Galaxy Nexus removes the automatic stock recovery flash that you linked to.  You no longer have to do anything special to keep CWM installed when running stock.