So, I'm back from my holidays, glad you kids are getting along ;-)
Put something like this (warning: untested) in wp-content/cache/autoptimize/.htaccess:
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule (.*) "-" [G,NC]
</IfModule>If this works, you'll probably want to update /wp-content/plugins/autoptimize/classes/autoptimizeCache.php to have that code as well (as autoptimizeCache.php writes .htaccess if not there).
The question of missing JS-files on SEO is a good one, but I have no answer except that in general Google needs to understand JS in order to be able to crawl JS-only sites built in e.g. AngularJS or Ember.
hope this helps,
frank