Ouch, iCloud-only files show up fine on a spotlight search when offline as well. My bad and ignorance. Sorry.
Still, a "file" represents information, an app only enables me to read/edit/manage that information. A plain-text file can be opened by many apps and there are many valid reasons for me to do just that. If I need to search for a specific file I will have to use the current filesystem to somehow trigger a situation that allows me to switch to another app that will read the file in question. A solution like Dropbox works better in that situation.
If there was a 1:1 mapping for mime-type<->app something like iCloud would work fine but that's not a viable situation. Not just because there will sometimes be "read-only" situations (e.g. watch a movie) and sometimes an "edit" situations (edit said movie). But I might for several reasons have a need to relate some mime-types/file-types to others and unfortunately a file-centric system is currently simpler in that respect.
I need control over the data, the apps come later since some might work better than others, depending on the context.
I'm not saying hierarchical file systems are good, I'm just saying that making the border between online and offline invisible while hiding the underlying structure isn't there yet for many reasons.
Online-only is a no-go for may years to come. However, if Apple (or someone else) solve the problems with app-centric systems while managing to remove the barrier between online and offline, my interest will be piqued.