The issue ammo at the time was 158 grain +P lead hollowpoint. They carried what they were issued.
Most of them weren't carrying Model 13s. SSA McNeill had a personally owned 2 1/2 Model 19 and SA Mireles had a personally owned four inch 686.
SAs Dove and Grogan had SWAT Smith 459 9mms. Their issue was the 115 grain Silvertip.
The guns assigned to the agents involved in the shootout are listed in the first section of this compendium on pages 69 and 70, by model and serial number. The blacked out names are guys that were on the stakeout but not involved in the shooting.
Federal Bureau of Investigation - Freedom of Information Privacy Act
There were 17 agents involved in the rolling stakeout that day. There were shotguns and MP-5s and ARs amongst them. As it turned out, the guys who did the stop had pistols and shotguns. SSA McNeill elected not to use his 870, and later regretted it. SA Mireles used his, but it wasn't particularly effective. He shot a G-ride and some feet. He put their lights out by walking up to the car and firing that 686 into their heads and necks. The .38 ammo worked fine for that.
There was no policy that they couldn't have long guns with them. Most guys did. Some of these guys didn't. They all could have had one if they wanted to.
Believe me, if it happened today the air would be a-glitter with flying .223 and 10mm brass. Both guys would be swiss-cheesed, and people would be moaning about excessive force.
I work with agents that won't knock on a door without a 12 pound gadget laden M4 hanging around their neck. I still prefer a pistol for 95% of the work I do. I don't feel undergunned.
I'm amazed that this shootout still fascinates people almost a quarter century after it happened, and that so much bad information still gets passed around. Its not secret stuff - click the link above and read all about it. I remember long debates about what kind of gun Mireles carried, and Massad Ayoob weighing in with his recollection that Mireles told him it was a 686. Mas was right, but that info was readily available for those who would just search it out. (Keep your eye out for a four inch 686 with serial number AAH8939.)
To answer the OP's original question, the issue ammo was and is a good round. .357 Magnum ammo was authorized for carry as a reload, and for carry in the revolver with the permission of the Assistant Special Agent in Charge (ASAC). When I carried a revolver, I went ahead and loaded .357 Silvertips and carried the .38s in my backup. The rationale for the edict to carry .38s in .357 revolvers is probably boringly pragmatic - it worked, it was cheaper, and lots of guys were still carrying Model 10s and it made issue easier. Nothing more, nothing less.