This isn't a bug, it's a side effect of combat. Sometimes, your follower's weapon will get shot out of their hands. If that happens, there's a decent chance they won't pick it back up, especially if there's other weapons handy (such as on nearby enemy corpses).
I'm aware that companions can lose their weapons during combat, but as I wrote in the first post: He was actually carrying it, it just didn't show up in his inventory, only on his dead body. After reloading my savegame it didn't show up on his body anymore.
Yeah I avoid giving followers unique weapons simply because I've seen them shot out of their hands... and bounce down a cliff. Happened to me on the hill near nelson and I could never find the thing again; I even had rex with me so I could look for the green highlight in hopes of finding it.
In Fallout 1&2 your companions could drop their weapon after a critical miss, sometimes it would disappear behind another sprite like your car. If you were really lucky you there was still one pixel sticking out. I guess the devs upgraded the 'pixel-hunt' to 3d standards
If it's a bug, then it's difficult to point out exactly and I can't say I'm 100% sure I didn't overlooked something. But being able to spawn the weapon at least provides an acceptable work-around. It does give me a nice idea for a mod though. A dialogue option to ask where his weapon is, and when he can't find it, you can send him to work in the Atomic Wrangler untill he has earned enough to pay you back

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