ATUM is not using http protocol anywhere. For all the internal URL building, ATUM is using this WP core function:
plugin_dir_url( __FILE__ ) )
That is the function that 90% of the plugins use to get an URL pointing to the plugin's path.
So, if this function is returning a http URL instead of https, it's not related to ATUM...
If you go to WordPress Settings >> General, what URLs you have for WordPress address and Site address?
Have them http or https?