This is what I use for my 'hidden' subclassing windows, dunno if that might help. Notice the Titlebar properties and the lack of the DialogTemplate* specification in the XML)
<Window Id="WndSubclass" Version="1">
<Position Width="0" Height="0"/>
WndSubclass = MsgPlus.CreateWnd('wndsubclass.xml', 'WndSubclass', 1);
Can't it be that the 'problem' is in that minimize-to-tray app itself, showing all windows instead of just windows which have a visible portion (size > 0x0), a title on the titlebar and/or buttons, and are actually visible, etc?
* Why do you need that anyways if the window is just for catching messages?. It has been a very long time since I played with interface windows so I can be wrong, but if you specifiy that isn't there stuff being drawn on the window? Is the shown XML the entire specification you use for those windows, or did you leave some stuff out in your post?
EDIT: I have just tested TrayIt! myself (with the sendTo script running), and it does not show the hidden subclass helper windows here on XP (as defined and used like the XML and JS code above), nor any other hidden window which exist (there are many of such windows on every system).
So, my guess is that you're doing something wrong with your JS-code or XML-code, or that you forgot to define some things (like those titlebar properties) or that you defined some things which actually make that subclass window visible (like the custom icons or dialog template definition).... You need to test these things yourself though, I don't have the time atm to do all this
PS: in some posts/articles about TrayIt!, it is said that it doesn't work as it should on Windows7 (but that's more about the changed tray system in Win7). Dunno what OS you're using, but maybe this can be the culprint too?