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...