Suppose you have most of your game created in js, but you are trying to reference a variable in a cs script. Using Find(otherObj).GetComponent(ScriptName) will automatically assume you are using the .js - how do you specify that you are using the .cs?
If you're having a problem with compile-time errors - Try creating a folder called "plugins" or "Plugins" (not sure if capitalization is important) and putting your .cs files in there. THat'll cause them to be compiled earlier than most other scripts, and your .js files will know about their variables.
It's not that Unity assumes you're using JS, it's that Unity hasn't compiled the CS files yet so it doesn't know about them.
I've never tried it, but I think Unity translate all your scripts in something standard, so every class are registred the same way, either they are from .cs or .js, and the Find() won't care about it. That's what I think anyway.