I haven’t done this kind of a hook yet but I did find this page in the wordpress codex
https://codex.wordpress.org/Function_Reference/wpmu_welcome_user_notification
They do explain a bit their about how you can modify the content of the activation and notifcation emails
I will try to explain a bit here
In WordPress an Action is a type of hook. You get Action Hooks and Filter Hooks
Actions are triggered by specific events that happen in WordPress like when a post is published you can trigger a custom action. Linked to a function that handles what you need it to do. An idea here is say for instance you would like to update a third party database when a specific post is updated you could link that to an action. Actions are hooks to WordPress using add_action()
Filters are functions defined for WordPress to run data through as it is displayed. So say for instance you would like to change some text on a post without affecting the database you would use a filter. That way when you change the filter you don’t have to edit the actual database values of the posts. Filters are hooked into wordpress using add_filter()
For more information I think have a read at this page
https://codex.wordpress.org/Plugin_API
which explains more in details about Hooks.