All tournaments develop bad habits because they have rules. In kyokushin you are encouraged to keep you hands up, although the way this is done in kyokushin tournaments does not provide a good defence for punches to the head. Because there are no punches to the head ppl in kyokushin tournaments can stand relatively close to eichother and make combo's to the body. Headpunches would change this game of course.

As for training, it depends on the dojo how much attention is being paid to head punches. It's currently accepted by the majority of martial artist that you have to crosstrain or do a NHB kind of style if your purpose is to be the strongest fighter alive though.

On the following website you can find a page called "the rise and fall of kyokushin", which actually gives an interesting overview of some achievements of kyokushin against MT fighters for example:
Bottom line of the page is that the early kyokushin fighters (e.g Oyama himself) who had great success, had experience with both punches to the head and some judo, which made their success possible.
Since it's a kung fu website, it wants to make the point that kung fu is teh deadliest though, so they do tend to focus a bit more on the shortcomings of kyokushin.