From what I have seen, those small places normally requires a deposit, and not sure those reviews are real. I wrote some reviews at TA at hotels that I stayed in and they got rejected for no reason. I have stayed in hotels that are highly rated by TA and got disappointed. TA was good about 2years ago but now I think it's getting too commercialised.
It's true that booking.com sells a lot of small hotels that no other major hotel sites does. Those German B&B are normally available through German sites and if they sell through booking.com they could reach more potential customers.
Another thing I like about booking.com is they state hotel policies very clearly, even better than the hotel's own page. We have 3 small kids and we don't want to rent 2 rooms so browsing through booking.com would give us an idea if it's ok that we all stay in 1 room.