The unfortunate answer is that I don’t think there’s anything you can really do to prevent this.
Assuming we’re talking about a Linux based server as the destination for your theme, the umask settings for the ftp user determines the permissions for new files, such as a fresh upload of your theme’s files.
It also could be affected by whether or not the ftp user being used to upload the files (who will also be the owner of the file) is the same as the user running WordPress or in the same group. However if there is any sanity in their server setup all those files should be readable by all users, but it sounds like your issues with JavaScript files suggest that isn’t the case.