I honestly don't see what's wrong with him still using the PPK. I'm no gun expert but neither are most people watching these films.
One already believes Bond a deadly shot, therefore is able to make just about any gun effective against somebody. People don't really correlate deadliness with functionality on film, because on screen, it's about how the characters use the gun or the pre-existing knowledge of the character's skilled background. Bond being a prime example. It's really not much of a stretch for him to still use it. If you want to increase its deadliness, you can stretch the believably of it a little bit. But I imagine that's more in Bond's skill rather than its firing power. Unless he's thrown in a situation where clearly a PPK is outmatched, then he will use a better weapon which we've seen already.
So pretty much, it's never really been much of an issue. The only way it can be unless the firing power is explained, then you get into that technical territory where one may have to reconcile those details.