lately (probably since 4.3.4) I've noticed all my hidden files within the WoW folder are having their hidden attribute cleared when I run the launcher. This goes for both files that belongs to the game, as well as any I create myself. I'm using 64 bit Windows 7.
It's not just the "Hidden" attribute; the Launcher also removes the "Read-only" and "System" attributes, which breaks custom folder icons and causes .svn folders to be shown (possibly the main symptom you're seeing as well).
The only reply I got was some random guy giving me dire warnings about the consequences of not using the Launcher. :(
However, I've never noticed any issues launching WoW directly, either now or in the past as I've quit using the Launcher since I identified it as the cause of unwanted folder attribute removal, but had only started using it after the recent "Reconfiguring game files" patch so my solution has been to simply not use the Launcher.
Afther following the instructions there, you can use this command to hide all your .svn folders (and give them the "System" attribute, so you can theoretically show hidden files, but not see the .svn folders as long as you leave the "Hide protected operating system files" option enabled):
It's not just the "Hidden" attribute; the Launcher also removes the "Read-only" and "System" attributes...
It probably also removes the "Archive" attribute, but that doesn't really do anything unless you're using certain backup utilities or command-line utilities, so for normal users that one is irrelevant.
As for marking .svn folders as System objects, the only benefit is that you still won't see them if you enable "Show hidden files and folders", as long as you don't disable "Hide protected operating system files". I find this useful because there are some circumstances where I want to see hidden files, but effectively zero circumstances where I care to see .svn folders, and this lets me filter them out. If you don't want this additional level of visibility filtering, you can leave out the [FONT="PT Mono, Consolas, Courier New, monospace"]+S[/FONT] flag when you run [FONT="PT Mono, Consolas, Courier New, monospace"]attrib[/FONT].
In any case, despite all of the stern recommendations from Blizzard and random forum know-it-alls, I have yet to see an actual explanation of what the Launcher does or why it's important. I've never had problems while not using it, while in the few months I did use it, I had nothing but problems (file attributes being removed, "could not connect to update server" errors, etc.) and felt like I was just wasting my time clicking through it all the time, not to mention having my eardrums assaulted by the obscenely loud noise when you click "Play"... which they still have not managed or bothered to fix. :(
The MoP beta launcher does not exhibit this obnoxious behavior. Hopefully this is an intentional change, or at least one that will persist through the end of beta and make it into the release launcher...