Katawa Shoujo Forums

While I have no direct experience, I've always heard (and see referenced on the internet) that in Japan, hankerchiefs are seen as unhygenic, and either tissues or even paper is used and thrown away instead of being re-used. Maybe the Japanese team could comment. Whether it's worth changing the text to use tissues is another question.

Added: Hisao sometimes waves hello instead of bows, which usually means "come here" in Japan (e.g. scene Message Passing in Shizune path)