I'm annoyed that .wine is inaccessible through KDE and Gnome apps.
It is accessible all right. You just don't know how to get there.
Not through the file manager, but often in various applications.
nope. Unless you're talking about some very broken applications that I didn't come across yet.
It's not wine's fault per se that those apps lack a "show hidden folders" option
KDE applications hopefully use KDE's open/save dialog, and there it's a matter of pressing F8 to hide/unhide hidden files.
I'm sure Gnome has something similar, but I don't use it so I didn't bother looking the key up.
I.e. no big deal.
Cheers, Kuba