[Quoth]

We have no way of knowing what feedback Kobo got and how accurate any reason they give for anything. Don't shoot the messenger! (Davidfor).

Unlike a modern Smartphone, tablet or laptop an eink based ereader is certainly not a general purpose device. So this directory scanning issue isn't going to affect most users.
It's hardly going to affect anyone. So much so I wonder why Kobo bothered. I'd wonder even if the real reason was something other than what was communicated, which might have been a second hand verbal comment.

I can't see it's worth getting fussed about one way or the other. It does seem like a pointless change, but for all most everyone only using the ereader, even with Calibre or USB transfer (sideloading) direct from Gutenberg or Smashwords rather than WiFi from Kobo, it will have no effect.

I use Linux, I've used Windows and UNIX in the past. I don't have a problem either way with the way it worked before or now.

I'd say anyone using a computer to sideload (USB copy) is going to search on the web or even (SHOCK) read manual and discover where to put books in the past if they didn't appear.
The biggest advantage after all of the Kobo ereader isn't the Kobo store, but about 50,000 popular genuinely out of copyright books converted to epub.