Fixed an error in the question regarding the subquery. Should make more sense now.

->with(['children' => function ($query)
{
   $query->take(3);
}])

will take 3, but for whole collection.

I would make a new relationship something like children3

return $this->hasMany('App\Message', 'parent_id', 'id')->take(3);

and then

$messages = Message::select('messages.*')
        ->where('post_id', 1)
        ->where('parent_id', 0)
        ->with('children3')
        ->paginate(10);

I tried your recommendation (children3), but it's still only returning a total of 3 children (i.e. only for the first parent result).

Anyone?

Anybody?