Only process values in config entity query conditions for values that have values

The change in MR!2585 fixes the error for me. Thanks!

if you goto /admin/module
enable a module with dependencies
when you click on the button the first time it will show you the dependencies
on that page is a button to install
when you click on it, you are taken to the admin/module page and nothing has happened. no modules were enabled

Per #7

Also will probably need a test case to cover this change.