Links are not part of Septera. And which plugins are you referring to?
All the links which are displayed in content are part of the content added to the site (menu, widgets, pages/posts) so they are under your control.
Those used by WordPress (for the styles, scripts, some media, so on) are dependent on the URL you installed WordPress at and can be updated to use HTTPS if needed.
You can find information for this procedure in the official WordPress.org forums and the documentation:
https://make.wordpress.org/support/user-manual/web-publishing/https-for-wordpress/