For wood panels it looks silly with them on the bottom. For metal, on bottom is the way to go. Here is a wood panel without dust cover on top. Looks terrible. I guess you could router the bottom and flush up the stick some, but not a lot of operators took the time to do that.
I remember the 4P games having them on top (TMNT, X-Men, Simpsons, Captain America, etc)... not that they couldn't have been changed, but it seems unlikely that it was that common. I remember spinning the dust covers while waiting for cutscenes and stuff.
You can clearly see them in the Captain America Flyer: http://flyers.arcade-museum.com/?page=flyer&db=videodb&id=1573&image=1 ... not that flyers can't be different than the actual games, but I'd say a flyer is probably the best way to see how it actually was, unless someone's got a NOS cabinet somewhere that we can unbox.