This isn't that hard to grasp.
1) The terminal performance of 9mm has come a long way since the 80's and 90's where it didn't fare so well.
2) For all intents and purposes, all handguns are weak and not our first choice to stop a threat. All handgun calibers essentially perform the same.
3) If they perform the same, then you get some HUGE advantages from the mass issue of 9mm handguns.
a) More ammo per gun/magazine
b) Easier caliber to master/shoot well
c) Less expensive for agency and individual purchases
d) Less damage/wear on the weapons (saving money on maintenance and replacements)
e) More universally available (think worldwide). Anyone want to guess what agents are issued when they deploy OCONUS? That's right, they leave the G22 at home and take a G17 with them.
f) Faster follow-up shots (since we all know handguns suck at putting down 2 legged predators)
An interesting fact many may not know about is that the FBI issued 40S&W duty ammo is downloaded by approximately 100fps. The current 180gr Ranger, and the previous 165gr Gold Dots that are bought by the agency are slower than the same ammo when purchases at Bass Pro or Wal-Mart. This was to make it easier to shoot. Not the best idea IMHO, but then they don't care what I think.
Also, remember we are discussing an agency with 13,000 or so sworn. That's a lot of guns, ammo, and time to get agents ready for the street. Using 9mm is a win for that scenario.
The bottom line is that the difference is not worth the debate that will always ensue when people get their feelings hurt because agency XYZ doesn't use their favorite ABC bullet/caliber... This is in no way a step backwards in time as some have suggested. If we should be surprised by anything, it's that they are doing something that actually makes perfect sense.