I think that the thought process is that you want the black boxes to remain with the bulk of the AC. You find one you find both. Ejecting them doesn't really make much sense, and while floating them does in some ways, drift would cause them to travel pretty far from the wreckage. Plus, they're going to be diving to bring up important bits of the AC and bodies anyway. That said, it does seem like a fuselage mounted marker body that detaches from the AC when submerged seems like a swell idea.
Oh, and the next step in the evolution of telemetry is going to be to have the AC burst transmit the FDR/CVR data to satellites. That will provide timelier info but will likely introduce other problems, as well.