We know the reason(s) that ZUN can't able to re-release PC-98 games because one; he doesn't care, but also two; he would be in deep legal trouble, since he made copyright infringements of other series for Touhou like the background of Makai Stage 16-19, Ellen being the copy-and-paste of a manga character, some programming codes from other games, etc. So what is he going to do to not have legal issues? Well... change some stuff of course, like changing the backgrounds, remove some references, add a new character as a substitute for Ellen, change the code to be more original and etc.
That's what I think, if he wants to re-release them for the current fanbase.