These things being taken down is an eventuality no one can avoid, however if no one but Nintendo sees it, and takes it down, not many people will know about it.
By spreading these things when they are good it encourages a lot of things. It encourages backups, communities dedicated to preservation of files or at least discussion of them (through piracy of course, though still counts). Making more people aware of them also makes some talented individuals realise that they have the capability to get into these things themselves. Etc.

I for one had no idea about this prior to this post, and Super Mario: Sunshine is one of my favourite games, so I'm excited to try this mod out later.