It has been far too long for me to recall all the details on this issue. The only thing that I can recall is that the search path for FTL files is different than those for JS files. If WebWork is looking for a template it looks in the /template/<theme> for overrides and then in classpath. When it looks for JS files it searches the classpath only. So, overrides need to be placed in the /WEB-INF/classes directory since this ends up in the web application classpath prior to the webwork JAR files.
I see your point about changing the JS URL in the FTL file to NOT use the /struts namespace, but if I want to use a theme (say XHTML) and don't need to tweak it at all, it would be nice to have the ability to override JS files in the same manner as I can override FTL files, by placing them in the /template/<theme> and it searches there first and then falls back to the classpath. This would standardize the override method for both types of files.