I've heard the same thing, from inside the Bureau. Nothing official, and I doubt anything will happen until the whole budget fiasco is worked out.
We issue 9mm, .40, .45, and 10mm (for the MP5/10) now, so it would just be a matter of changing the amount of future orders. I've been through a few gun changes (1076 to Sig to Glock) and its done mostly by attrition. New guys get the new guns, as old guy's guns are sent in for maintenance they get swapped out, and agents retire and their guns get smelted.
The current 9mm load is a 147 grain Gold Dot, so that is most likely what the new issue would be.
I suspect .40s will remain in the inventory for a long time, maybe only as POWs (personally owned weapons).
As far as FBI ammo supply goes, it is the lowest I've seen in 22 years. Play ammo used to be a nice bennie, now it is mostly a thing of the past. Budget reasons. The billion round order silliness has been beaten to death. Its just contracting, and its just DHS, not the Bureau. The gun store ammo shelves are groaning with .40 ammo in my neck of the woods - the only thing still scarce is rimfire ammo - so if it was a nefarious plot to keep ammo out of the hands of citizens it didn't work very well.
FYI, Bureau agents have always been armed when needed, even prior to the legislation that codified the practice. Being armed was considered a part of the job, and agents engaged in shootouts before Hoover even took over. What legislation authorized the U.S. Marshal's to be armed?
The above is my personal reflection and not the opinion of the Bureau.