Yes, you did indeed see a 747-400, as you say it is known as 'Domestic' and is an upgraded version of the earlier 747SR (Short Range) model, used specifically on Japanese domestic services.
The winglet feature that is present on normal 747-400 models is designed as a performance enhancing feature to improve the aircraft's range and fuel consumption, as well as a number of other factors. These requirements are therefore mandatory for an aircraft operating on services of anything up to 13,000km.
The 747-400D model does not require the winglet feature as the routes that it serves are within a distance of 1000 - 3000km.
As a 747D (or SR) begins to age, it is entirely possible for the manufacturer to retrofit winglets, etc to the aircraft so that it can operate on long haul routes, of which the airframe had not previously been exposed to, therefore prolonging the aircraft's life. The aircraft would then be redesignated as a standard 747-400 or 747-200 or 300.
I love it when a plan comes together