First of all, to a question like this - there are no correct answers. As we do not know what went through van Gaal's head, we can merely speculate.
One reason could be that Cillessen hasn't saved a single penalty during his professional career, as a dutch newspaper reported. However, if I'm not mistaken, Tim Krul hasn't got a very good record neither - so this is likely to be only a small factor.
Another reason could be the difference in height between the two goalies, but in my opinion and experience - that's not a very important factor. There are many important characteristics, but as long as you're taller than 1,85 m - height is not amongst the top three.
I believe the substitution was based on a mental factor and on preparation. It's likely that the coaching staff did not prepare Cillessen for penalties, to have him a hundred percent focused on the first 90 minutes (and extra-time). Preparing a goalie for penalties means placing some of the focus on an eventuality, which is not preferable. Instead, they probably chose to prepare Krul for the eventuality of a penalty shoot-out (reports say that Krul was informed on forehand, that he might be put on if it came to a shoot-out - but Cillessen was unaware that he was to be taken off). Krul had probably spent hours studying the opponents penalty-taking-techniques et cetera, and was thus better prepared (mentally, educationwise and physically).
Also, one must recognize the fact that Holland doesn't have an overflow of high-class substitutes. If they had, van Gaal would probably have put on some fresh legs during the extra time, instead of "wasting" a substitution on changing keepers.
Please note that this is only speculation, and that it's impossible to determine the truth without actually spending some time inside the heads of the Holland coaching staff. The theories above are simply my subjective ones!