The problem has nothing to do with whether Kovid is "getting weary of it" -- if he's weary of anything, it's of people who don't understand that calibre manages their books, and want to reach inside it and mess with calibre's files. There would be nothing to be gained by making it easier for users to muck around with the file database's private innards, and a great deal to be lost, not only in initial coding effort, but in subsequent support requests from people who screwed it up and corrupted the database, bricked calibre, or whatever.
Personally, I'd vote for using numerical folder names, rot-13 shifting the file names, and giving them cryptic extensions, so that users would keep their grubby hands out. It's the fact that the names are human-readable that makes humans want to mess with them. People, or at least ordinary users, don't try to fool around with the insides of the SQLite databases that calibre uses -- they understand those belong to calibre. But the files look like what they're accustomed to thinking of as "books", so they want to access them directly.
Calibre is ready and willing to export any books you happen to want externally as files of your preferred format. That's how those files should be accessed -- not by peeking up calibre's skirt. It'll slap you.
Why is it, by the way, that it is people who want changes to this one aspect of calibre, and only the people who want those specific changes, think that insulting Kovid (and by extension the other calibre developers) is the way to go about it? We've had a bit of a break lately, but at one point we were getting post like that every week or two, ranging from direct, in-the-face insults to insinuations like yours that the only reason Kovid doesn't change calibre to work the way you want it to is that he's lazy or just bored with it. I expect that from 10-karma newbies, not from someone who's been here longer than most of us (and way, way longer than me).