To name and shame some culprits (the one's who have shame, I won't name java because I won't expect them to care) 1) Mozilla 2) Gnome 3) Gimp 4) GPG 5) Thunderbird (Why is there a sep directory and not under .mozilla) 6) mplayer I guess one reason why this occurs is that it's easier for to be carelessly cross-platform this way. Except you'd expect better from mozilla, specially because they store Windows stuff very w…
Why not _shame_ openssh? Or vim? Or emacs? I would advise not calling for shame on any of these projects because they have a pattern to support that has been in place longer than the XDG standard has been in place. You can change gnupg's home dir, but it would break a lot of currently functional setups if it just moved.
You can just change the default: if .gnupg exists, write everything to it. If not, write to $XDG_CONFIG_HOME/gnupg/ and $XDG_DATA_HOME/gnupg/ as appropriate (deciding how to carry out the split is not obvious, but can be done).
I agree, though, that calling it "shaming" is neither justified, nor useful.