Think of this as a "meta-filesystem". Instead of asking the OS for files and folders, an app just asks the OS for "photos" or "music". Most people, and by most people I am referring to the lowest common dominator like your grandmother, don't care where a file is and actually constantly loses where files are.
As with all things Mac, since Apple obviously dogfoods their systems and servers with their computers, the filesystem will not go away. But it will be hidden from the bottom 99% technical layperson who simply doesn't care. Files and Finder, like Terminal.app, will be there for those of us who do care.
You need to differentiate between what's good for the people/commoner and what's good for the developer/pro-user, since they are in extremely difference market segments given technical proficiency.
I guess my disagreement stems from the fact that I don't see what I type into those boxes as commands (even though some search boxes, like the one in the Windows start menu, can work that way). I think of those boxes as fixed to one command, search, and all I get to type are parameters.
Seriously though, from the user standpoint, typing "vim" into the shell and typing "TextMate" into Spotlight are more similar to each other than either of them are to navigating through the Finder and double-clicking TextMate, or even clicking it on the dock. The shell is smarter, but perhaps too smart for some users.
Loads. They are called working scientists. Sometimes there is a perception that the world is divided into geeks and "appliance" users. There is actually a non-trivial amount of grey area in between.
Not a snarky question: I'm not very familiar with scientific computing and am curious (from a UI perspective) why, say, applications for office work manage to keep things essentially all in the GUI, but apps used by scientists can't. Is the problem that scientific apps don't devote enough resources to good/comprehensive UI or is it that what scientists do is better done from a command line?
Regardless: as I said elsewhere in this thread, this is why I'm starting to think of PCs/Macs as the workstations of this era. There will always be a need for them. But they're probably needlessly complex for most uses.
An iPad running a terminal emulator and with a keyboard attached would be a comparable experience. Though, clearly, it's not the best solution for most such users. Linux/etc all the way for that.
Certainly in my area (astronomy) I have seen some attempts to provide gui based intefaces to data reduction, and even mocked up a few myself; but the effort to reward ratio isn't worth it - especially since you are dealing with people who can, in general, follow instructions.
Also, do not underestimate the higher effiency of the commandline - after all, there is a good reason we all use it. Even if there was a system administration gui out there, would most sysadmins use it? It's actually faster to type.
I think the "appliance" model of computing (eg. iPhone/iPad) is perfectly valid for a good percentage of the population at least for some of the time, but it won't render "classic" computers obsolete.
I also have to say that personally, I have generally been dissatisfied with attempts to disguise or flatten the filesystem by, for example, using tags instead. I actually think pretty damn hierarchically, so I often organise my material as IF it was a filesystem, when the application will allow me to do so - maybe it's just me?
Ask ten random Mac users how to find a file by name via the command line.