SC- what you're forgetting is that winglets are there to eliminate (or at least substanially reduce) wingtip vortices caused by air flowing around the edge of the wing from the high pressure area beneath to the lower pressure area on top. Sure, sticking something into the airflow will increase drag, but in this case the increase in drag is more than cancelled out by the decrease in drag caused by the reduction of the wingtip vortices - in all stages of flight.
Warlock's quote above from the MEL - "increase fuel consumption by 1%" - says it all.
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