Hostelbookers.com says that they charge "no booking fees", but I've heard that hostels don't receive the 10% "deposit" they charge. Is this 10% really a booking fee?
Yes and no.
Yes, because the 10% deposit they charge indeed goes to Hostelbookers.com, not the hotel. (See this thread.)
No, because you, the backpacker, don't pay any extra. You can pay (say) $20 to book via HW, in which case HW takes $2 and the hostel keeps $18, or you can pay $20 to the hostel directly and they keep all of it. I presume HW insists on this as a condition of listing with them, precisely so that they can advertise "no booking fee" and get as much business as possible.
In either case, you're paying the same $20, with no additional charges to you. Compare this with some airline booking engines like Webjet, where you pay the regular cost of the ticket plus the engine's booking fee on top of that, and could have saved money by booking with the airline directly.