確認バージョンは Laravel 7.26.1

例えばこんなモデルがあったとすると

class User extends Authenticatable
{
    /**
     * Relations
     */
    public function posts()
    {
        return $this->hasMany(Post::class);
    }

    public function comments()
    {
        return $this->hasMany(Comment::class);
    }
}

class Post extends Model
{
    use SoftDeletes;

    /**
     * Relations
     */
    public function user()
    {
        return $this->belongsTo(User::class);
    }

    public function comments()
    {
        return $this->hasMany(Comment::class);
    }
}

class Comment extends Model
{
    const UPDATED_AT = null;

    /**
     * Relations
     */
    public function user()
    {
        return $this->belongsTo(User::class);
    }

    public function post()
    {
        return $this->belongsTo(Post::class);
    }
}

一階層のhas

    User::has('posts')->get();

select * from users
where exists (
    select * from posts
    where users.id = posts.user_id
    and posts.deleted_at is null
)

二階層のhas

    User::has('posts.comments')->get();

select * from users
where exists (
    select * from posts
    where users.id = posts.user_id
    and exists (
        select * from comments
        where posts.id = comments.post_id
    )
    and posts.deleted_at is null
)

一階層＆二階層のhas

    User::has('posts')
        ->has('posts.comments')
        ->get();

select * from users
where exists (
    select * from posts
    where users.id = posts.user_id
    and posts.deleted_at is null
)
and exists (
    select * from posts
    where users.id = posts.user_id
    and exists (
        select * from comments
        where posts.id = comments.post_id
    )
    and posts.deleted_at is null
)

上記の通り、一階層と二階層両方書く必要はないです！