I'm not an expert at modding Elite Force other than swapping out textures or sounds, but I think I found what you'll need to change to modify the damage - you would probably need to change the weapons damage.
In the pak0.pk3 file (you can open with WinRAR), you'll want to go to "botfiles" and the open "weapons.c" in notepad. If you scroll down the text, you'll see the damage numbers for each weapon. Modify it to your liking, save as "weapons.c" on your desktop and then save it to a new .pk3 archive in a new "botfiles" folder - this will overwrite the old one.
I make no guarantees that this will work, this is just from a quick glance at the files. Let me know how it goes.