At the time that the 400 model was conceived in the mid-late eighties, winglets and computers were becoming the must-have fashion items for new aircraft. To spruce up the 300 model, Boeing decided to add winglets to pretty much the same old wing design that they had since the introduction of the first 747 model.
As a result of the lack of aerodynamic optimization, the winglets only provided a modest improvement (reduction in drag) in fuel flow to compensate for the additional weight (approx 1200 lbs per winglet from memory) of the winglets over long sectors. But they looked good to the customers.
However, for short sectors the reduction in drag did not compensate for the increased fuel burn for the extra weight. For this reason, some Japanese domestic operators ordered their 747-400 models without winglets.