Not every frequency listed in a repeater map for a Con+ system is used, in my experience. I may be wrong on this too, but, I believe its for either "future expansion", the ability to take a frequency from one site and move it to another if needed (if the license allows is). Not saying this is the case, but, look at Site 14, it uses LCN 3,5,6. Theoretically speaking, 1,2,4 could/were used there, and as the system needs changed, they could/did push out a new repeater map with more frequencies, adding 5 & 6, either new or from elsewhere, assigned to that site, move the equipment, get it up and running, update the site information there, and then 1,2,4 could be seamlessly taken offline without any hiccups, and that equipment or frequency could be used elsewhere. Site 1 is a good example of it. Site 1, busy site, basically the "main site" where a TON of traffic is on, has a ton of frequencies, more even listed on the repeater map, but not all of them are used.
Could be wrong, but that's my understanding and logic of the "madness"