I am only a few hours in and just found the Fanghammer, or what was it called. I just had it disappear while swapping between the elk and my own inventory (hence, I cannot look up what the weapon was actually called).
Is this something that is rare to happen? I don't feel finding weapons is a problem in the game, but it will be annoying if this will happen very often...

The steam forums also mention an easy like this, but there the dev mentions it will be fixed in a next update (and this was about 1.03 or earlier, not the current version). I am on 1.05, so can I assume this should be fixed (for the most part)?

Just an annoying thing: the main menu mentions some other build number (1.4.16_3), instead of the versions mentioned in steam or gog (1.01, 1.03, 1.05)

Unfortunately, I don't. I was switching around weapons pretty frantically, so not sure it was to or from the elk.
It also didn't happen again in the couple of hours of platime after, so it is probably rare or only happens when handling inventory so frantically as I was at that time.

I don't know if this is the same issue as the OP, but yesterday I had a similar issue with an item disappearing from my inventory. Here's what I did to produce it:
– In the elk's inventory, I had stored a two-handed weapon and a shield.
– Ada had a two-handed weapon equipped
– I tried to equipped the shield and it succeeded
– The previously equipped two-handed weapon was sent to the elk's inventory (Yes, I was seeing 2 two-handed weapons in the inventory which is illegal)
– When I tried to equipped back one of the two-handed weapons, the other one disappeared from the inventory

Thankfully, I'm playing on PC, and I had a backup of my saves, so nothing was lost. I tried to reproduce this behavior multiple times but the game correctly prevented me from switching the shield because there already was a weapon in the inventory. It seems like there is a very rare condition at play here where you can end up with an inventory in an illegal state which will result in a loss of item.

I had the following equipment:
– One-handed weapon: Blade of Agadah
– Two-handed weapon: King's Guard Sword
– Armor: King's Guard Armor Set
– Additional weapon/armor: empty
– Elk inventory: King's Guard Halberd, Keeper of Nomos, and Bow of Bark

As I said, I tried to equip the Keeper of Nomos and for some reason the game accepted to do it even though it should not. And I ended up with both the King's Guard Sword and the King's Guard Halberd in the inventory. If I remember correctly, when I tried to equip the sword back, it disappeared and I actually equipped the halberd. I never was able to reproduce this.

However, while playing yesterday, I ended up in an even bizarre situation. I think my equipment was:
– One-handed weapon: Blade of Agadah
– Two-handed weapon: Keeper of Nomos
– Armor: King's Guard Armor Set
– Additional weapon/armor: Bow of Bark
– Elk inventory: King's Guard Sword

I'm not sure exactly what I did but ultimately when I opened my inventory, the King's Guard Sword was gone and instead I saw a second Keeper of Nomos. Yes, I know that sounds crazy but my interface was really displaying a second shield instead of my sword! I dropped it on the floor and it was really a shield...

So yes, there are stills issues with the elk's inventory, they are rare and hard to reproduce but still it could be a real issue for people who don't or can't backup their savegames.