I've got a third party wireless pad on ps3 that was cheap and it needs a USB dongle to work. There was an earlier version that worked directly with PS3 but a firmware update removed compatibility with it. I think Sony are keen to prevent third parties making controllers unless they allow it. Mostly I think they have been unique controllers that have been allowed which offer something slightly different than the regular sony dualshock.
I would guess the normal procedure is a hardware manufacturer submits their product to Sony, Sony decide whether it will be licensed for use and if they agree the hardware manufacturer pays Sony a royalty on each sold. Sony then fully supports that product as compatible. I'm sure Sony makes more money making the product than receiving licensing fees so would likely prefer to keep the new dual shock as the main controller for the ps4.
