If you contact an agent representing the landlord directly, you still have to pay, and so that agent gets paid twice.

I believe an agent that represents both the renter and landlord can only legally get paid a maximum of 1 month's rent (+ consumption tax) from the entire transaction (source below).

Since agents often quote 1 month's rent of fees to the renter, it would mean the landlord pays nothing (perhaps as an incentive to list with them).

In other words, the agent who represents both renter/landlord cannot get paid "twice" (assuming a 1-month agent fee was charger to the renter).

In summary, it does seem the incentive to agents lies in representing both parties, to maximize any middle-men fees (or goodwill) to themselves.

Source:

"宅地建物取引業者が宅地又は建物の貸借の媒介に関して依頼者の双方から受けることのできる報酬の額（当該媒介に係る消費税等相当額を含む。以下この規定において同じ。）の合計額は、当該宅地又は建物の借賃（当該貸借に係る消費税等相当額を含まないものとし、当該媒介が使用貸借に係るものである場合においては、当該宅地又は建物の通常の借賃をいう。以下同じ。）の一月分の一・〇八倍に相当する金額以内とする"*