What process do pro pilots have to go through with their passports when on the clock? Are they afforded any shortcuts or do they have to go through security EVERY SINGLE TIME?
Pilots (and aircrew) usually go through an expedited security screening, usually separate from passengers, in order to reduce wait times.
For example, US TSA has a program called the Known Crewmember Program that allows pilots and crew members to bypass normal (passenger) security line.
Pilots (and aircrew) have to show the documents as required by the local authorities. Usually, this will be the passport/visa or General Deceleration. This varies from country to country.
Pilot and author Patrick Smith covers this subject in his online column Ask the Pilot:
"But of all the half-baked measures we’ve grown accustomed to, few are sillier than the policy decreeing that pilots and flight attendants undergo the same x-ray and metal detector screening as passengers...An airline pilot who once flew bombers armed with nuclear weapons is not to be trusted and is marched through the metal detectors. But those who cater the galleys, sling the suitcases, and sweep out the aisles, have for years been able to saunter onto the tarmac unmolested. If there has been a more ringing, let-me-get-this-straight scenario anywhere in the realm of airport security, I’d like to hear it."