On a new design, the wings may be sufficiently advanced that winglets don't make an appreciable difference.
On an older design (eg 727), it may be a matter of not being able to recover the cost of designing, certifying and installing winglets.
Notice that the 777 and 787 have simpler designs (raked wingtips) and older airplanes have the horrific looking blended winglets that seem to be in vogue nowadays.