For a B747-400 the winglets become cost effective on flights of five hours or more. On shorter flights the cost of carrying the extra weight does not compensate for the fuel efficiency. I believe that JAL operate some 744's without winglets, but with modified wingtips, on their domestic routes.
The 744's with winglets are certified to fly with one winglet missing, but not both missing. Boeing could not justify the certification flying that would have been required for both to be removed, as they felt that it would be unlikely for both winglets to be damaged. The aerodynamics of an aircraft with the winglet removed is different to an aircraft with the modified wingtip.