The older the movie the more likely that it was real - as long as it looks real. I've seen poorly staged spankings in a few old movies where it was clear that there were only pats landing.
More recent movies have effects. Padded seats, fake instruments, or a combination of the two. Often the method is mentioned in the DVD's commentary. For example, the True Grit remake included padding. The Ya Ya Sisterhood scene involved a light piece of velvet that was made to look like a leather belt but couldn't be felt.
Then you have stories that generally come from the 60s or earlier. If I recall correctly, after the coal scuttle bit Maureen O'Hara threatened to sue John Wayne for assault if he ever tried something like that again. Then there's the story about Cheaper by the Dozen. The young actor Jimmy Hunt was reportedly acting full of himself and Clifton Webb, the on screen father, decided they needed to "rehearse" a spanking scene.
Darn, some of the great "spanking movie" pages have died. The closest I can find for the Cheaper by the Dozen bit is from a web page on Jimmy Hunt at
http://reocities.com/Hollywood/hills/3447/trivia.htm where it states:
During rehearsal's on Cheaper by the Dozen, Clifton Webb had to spank Jimmy for one of the scenes, but Jimmy states that he spanked him hard and he didn't like it. From then on, Jimmy wanted all rehearsals to be short, "Let's do the shot."
Goodgulf