I'm symlinking only the data dir, and what seems to work really fine for me is:

.) patch the 'main' wow (the one in the symlinks point to)
.) copy everything in the root directory of the main wow folder to the other folders (wow.exe et al)
.) delete the cache dir on the symlink dirs.

That's all I do, and it works like a charm.

There is nothing really interesting in the wtf or other dirs that gets changed on patches.

kind regards