Yes these functions are now being handled by advanced cockpit automation. There are a number of aircraft that have been either manufactured or modified to the two-man cockpit. The C-130J has eliminated the Flight Engineer and Navigator's positions, through the use of automation. The C-130J's aircraft systems have also been greatly improved to accept the automation. Since we are going to a new Global Air Traffic Management System, for the NAS, most aircraft are or will be configured to use this system. This system is or will be designed to mitigate or relieve some of the present and future air traffic congestion. It will allow for greater air traffic separation, both vertically and horizontally. It will allow flight crews to better plan their routes instead of tradionally following one aircraft after another on the present flight planning routes. Say for instance, you have a faster airplane and is able to fly higher than what is now normally planned. With the advanced air traffic management system, you will be able to take advantage of the higher altitude and fuel savings from it, and get to the final destination much quicker, by planning your own route. your new air route would be airspace that is presently not being used because there is no way to track aircraft in that space. The Global Air Traffic Management system will use GPS and another system that I can't remember right now, to keep track of those free flight airspaces, most desirable to be used. Altought the C-130 will be the most difficult to factor into this system, the current plans are for the Boeing Company, (through the C-130 AMP program) to modify all remaining C-130E/H models with a new avionics suite that will eliminate the Navigator's position, up-grade the cockpit to glass and automate the Flight Engineer's position.
By now you have heard that the DC-10 is being modified to an MD-10, primarliy for FedEx and entails converting it to a two-man cockpit just like the MD-11.
The C-17 has already been manufactured to this configuration and most of the Boeing fleet, with the exception fo the B-747.
There is more on this subject, but this should serve as a general answer to your question.