Is there a way to modify the prefixes in the chdk menu, so I could have a unique one for each camera?
No. CHDK cannot change the naming of camera jpegs at all. You can change the prefix of CHDK raw, but only from the options listed.
You could write a Lua script to rename files one the camera, but you would need to run it manually after shooting, and the renamed images might confuse the Canon firmware.