Good question! It depends on the place, and whether they've set themselves up for it. It looks like Yanbaru Hostel does have their own website: YANBARU HOSTEL
And they use another booking platform called Yadosys, which you can use to book directly with them: YANBARU HOSTELPlan List
Not all of the smaller (and more affordable) places have their own site or booking system, and rely on either call-in bookings (old school) or dedicated platforms like Hostelworld and Booking.com (which is in hot water of its own).
As a traveler, it's convenient to have a single log in and keep your reservations in one place, but if you really want to cut out these shifty middlemen, you could use the booking sites to find a hostel/hotel, then look and see if they have their own website you use to can book directly.