It apears to me that lots of websites dealing with lots of files (like music, pictures, news, books, ..) do not use hierarchical directory structure, but other forms of interfaces to get the user to those files user are interested in.
There is a broad variety of solutions out there and darvinistic selection of the fittest will show what user interface concepts are the good ones.
Websites do not need to wait until a new concept of userinterface gets integrated in Linux distributions, they just deploy their new website and users who are interested in the content of the website will use it and adopt to it.
The designer of the new website does have very powerfull tools to watch the users while they use the system to be able to improve its design.
Non of those is available to the developers of Nepomuk.
So it might be that people flock to SaaS offerings just because the ecosystem allows the developers to innovate much faster and makes available new features much faster to the users.