the only thing such programs can do (and are doing) is to encode/encrypt the source code with java. this is making stealing parts of the source code really hard, but this can not prevent downloading these sites. (everything that can be looked online can also be saved)
OE is quite good with general java scripts and updates with better support for complex java sites were promised aswell.
i had only one site i couldn?t download yet and this was one were all pathes where calculated with complex java, but i think OE will be able to handle these in the future aswell.