They wouldn't have shown it as a bare bottom one on TV, but if you are thinking about the continuity of the show, then if Sheldon was spanked on the bare bottom as a child he would have spanked her that way because (in his mind) there is only one right way to do anything.
But there would have been a second (non-FCC) problem with showing a bare bottom version - the multiple takes. By at least the second or third one there would have been marks visible when he tugged down her PJs.
Then again, they could have implied a bare bottom without showing, but we wouldn't have had a view of the hand smacking the bottom. From the right angle from Amy's front they could have shown Sheldon lowing Amy's PJs (or showed him doing something while saying "And I have to take your PJs down now" as Amy replied "Should I lift my hips"). Then, even if the actress had something on under her PJs, there would have been a implied bare bottom spanking.
Watching this episode, I couldn't help but think "So Blossom finally gets spanked", but maybe that's just me (for explanation, see
http://en.wikipedia.org/wiki/Blossom_%28TV_series%29 ).