I'm seeing similar issues. Using lxappearance or the lxde/xfce desktop tool to change the theme has no affect on Thunar's appearance. Checking both .gtkrc-2.0 and .config/gtk-3.0/settings.ini shows that the them is set correctly.
- Bug#921263: Thunar ignores dark theme Norman Ramsey
- Bug#921263: Info received (Thunar ignores dark theme) Norman Ramsey