I'm not sure if this is going to help clarify why some pictures show handles and others don't, all I've been able to find out is that they are called "EVA Handles" They are grab points for Extra Vehicular Activities.
http://www.sfgate.com/news/article/NASA-tries-to-get-a-handle-on-relic-auction-3051835.phpOne interesting bit of trivia, is that the EVA handles had a radioactive disk of promethium 147 which would glow so that they could still be able to see the grab handles if they had to do an EVA in darkness.
The location of the handles varied slightly depending on the mission plan, but I'd expect the two immediately below the main hatch would be common to multiple missions.
As to why there are pictures with the handles missing, I'd only be guessing, maybe they hadn't got round to putting them back? There was a disposal protocol for radio active materials, so it's likely the flight handles were removed because of the small amount of radio active material, and replaced with new handles for display purposes.
I'm going to agree partly with Humble_Scientist, and suggest that it's quite possible those particular handles have never been in space. But the rest certainly has.