Indeed, I have the same problem with the addon I'm working on.
Infantry addons based on OFP 1.46 or earlier use the pistol animations, sure, but like you said they aren't holding anything.
However, all the official BIS OFP units have been upgraded to use the pistols correctly.
My guess, when working on my addon, was to find the "new" upgraded version of the model that I based my unit on, xPack it, and swap out the textures with TextureP3D, like I always do.
I found my mc_sniperw2.p3d in the YourOFPDirectory/Res/Dta/Data3d.pbo file. Upon DePBOing that, I took the sniper model out and ran it through xPack. No problems so far.
I loaded it fine into TextureP3D and swapped out my new textures. So far so good.
I added some pistol ammo and a Glock in the config.cpp (except for the pistol code, the rest of the config.cpp was tested successfully in OFP 1.46) and StuffPBO'd it all back up. I tried putting the addon in the main OFP Addons directory, and then later on the Resistance Addons directory.
Both places, when launching a misson, I get a crash to desktop with this error:
"Warning: preNLOD format detected in /adsdelta/adsdelta.p3d". (adsdelta is my addon name)
My guess is that we can't use the same tools to unpack the p3d files anymore, or something. Maybe there's something that gets corrupted in the process.
Maybe it's something real easy and nobody's told me and you.
But it's too bad, because although it's technically a cosmetic problem it IS still an annoying problem.