If you are working with relationships, it's not a good idea to use MongoDB which is a noSQL database.
About your question, I think that it's not possible to eager load exactly as in a pure Laravel / MySQL application. The query is created and sent to one database.
As you need to retrieve the datas from 2 different databases, you can first retrieve data from MySQL.
// MySQL
$books = Book::all();
And then retrieve the related data from MongoDB.
$categoriesIds = array_unique($books->pluck('category_id')->toArray());
// MongoDB
// but here with perhaps another syntax appropriated with a MongoDB ORM (not sure that Eloquent can retrieve datas from MongoDB, never tested)
$categories = Category::whereIn('id', $categoriesIds)->get();