Surely this approach has some benefits, but has also some issues.
It's not really easy to use
If the target of your plugin are WordPress developers, they will be very familiar with plugin API, but end users are not.
For a non-developer, something like:
$data = give_me_the_data();
It's easier to understand, remember and type than:
$data = apply_filters( 'give_me_the_data' );
If you look at some of the questions on this site, you can understand how much confusion there is regarding action and filters in WordPress among newbie and non developers.
The "typo" issue
As a person that makes a lot of typos, I know that they are frustrating. If you write a function with a typo, it throws an error and the user immediately recognizes the problem. A typo in an action name will make the API fail but it's pretty hard to recognize.
$data = apply_filters('mp:get-user-data'); // works
$data = apply_filters('mo:get-user-data'); // does not work, hard to find why
$data = mp_get_user_data(); // works
$data = mo_get_user_data(); // does not work and throws an error, immediately found
The global hell
Actions and filters are just global variables. If you use them to build your API, your code can be f***ed up by any single other line of code present in the system.
It means that a bug in any who-knows-which plugin can make your plugin fail for no apparent reason. And the reason is that is not your plugin to fail.
do_action( 'mp:send-notification', $user_id, $message );
// somewhere else
add_action( 'all', 'do_something_bad_that_makes_your_plugin_fail');
Moreover, anyone can use those hooks and even if it may bring a lot of flexibility to your API, it also introduces a lot of complexity.
For example, if you use objects as arguments, being objects passed by reference, it's possible they are modified before your callback runs.
These are all the reasons that come now into my mind, but maybe there are other reasons if this approach is not widely used.
For me, I would not use this approach, especially for the last point, but I can not say it is absolutely wrong in WordPress context.
So I don't want to strongly discourage you in using it, just suggesting to consider all the issues in advance, because once you publicly release an API, it's very hard to switch.