The USAF originally needed the boom system so that thirsty USSR-bound B-52s could be refuelled at a much greater rate than is possible with the probe-and-drogue system.
Other large aircraft also use the boom method, due to the high onload rate and reduced time in contact.
But for fighters taking relatively small fuel onloads, the time between successive contacts of a receiver formation can be more critical than the actual time in contact, particularly if the receivers can take fuel at a decent rate... Hence 2 pods will be preferable to one boom and this also provides some system redundancy. Nevertheless, all fighter-type aircraft destined for the USAF and client states persist with the boom system, whereas USN and European receivers use the probe-and-drogue system. Some tankers, such as the KC-10 and (one of these days, perhaps...
) the KC-767A Pegasus and some KC-135 have both systems - as do most A330MRTT variants except AirTanker's Voyager...at present
But the worst of all options is the infamous BDA - a short hose attached to the boom. I only prodded against that once - in a 3-tank 8-missile Q fit F-4 without having had the benefit of any dual or even a briefing. I did actually manage it, but the inbound Bear had decided to turn back to Mother Russia...