The documentation seems a bit sparse but I don't think that OPCache is about caching compiled PHP bytecode, and this would not affect JS files because these are not PHP. I have always assumed that OPCache should be smart enough to invalidate a cached file if the file is altered.
If you are having difficulty with JS files getting cached, this might have something to do with your web server configuration? IIRC, apache might be configured to send cache directives for certain MIME types?