The invisible gun glitch got fixed for me after doing the following:

1. Enabled both vanilla and standard version of the mods settings on my MP server
2. Load into the game - some guns might've disappeared from your inventory, they will reappear at step 4.
3. Leave and disable the vanilla version
4. Rejoin, weapons should be visible now.

If this fails I'd also try to create the server once with both mods disabled.