On some servers i saw a green transparent weapons or ammo boxes in a place where the real weapon will spawn. Weapons wasn't also laying horizontal, but diagonal. How to set it on my own server?

That is custom mod someone wrote for Nexuiz. I have not yet seen a download link to it so i can't tell you how to setup your server. I think its the "All out war" server..
Here is more about the server and mod:
http://www.forums.alientrap.local/viewtopic.php?t=154
http://www.forums.alientrap.local/viewtopic.php?t=344
http://www.forums.alientrap.local/viewtopic.php?t=96