Firstly well done for checking on the COI and making sure of health tests etc, this is a sensible approach.
Although the KC provides breed averages, this will depend very much on the breed in question - for the numerically small and rarer breeds the COI may be higher due to dogs with similar pedigrees being used more often. This is not a bad thing per se, as long as new lines are added to the gene pool at some point.
Looking at the details you have provided, the highest COI on one side shows there has been line breeding in play. This is a common breeding techinique used. Before anyone jumps in and says it is just in breeding, it is not there is a subtle difference. In breeding is breeding very close relations together, which is not acceptable, line breeding is using dogs and bitches of similar lines. It has advantages of knowing health tests are continually good throughout the lines plus temperaments, conformation etc.
So on one side there has been line breeding, to ensure this does not become in breeding, every so often there will be a mating with a totally out cross, meaning no commonality of breeding within the pedigree, which is the 0% COI. This is a very sensible route to take. As you can see from the litter you are looking at, this had reduced the litters COI down to 5%.
Breeding is both an exact science and elements of luck - using a sire and dam with 5 generations of totally unrelated pedigrees is a real unknown but will produce a low COI. Using line breeding and/or line breeding and out crossing provides more insight into what may be produced in the litter.
Probably the adage better the devil you know is part of the science!
Visit the breeders, see the dam and any other relations. See if you can meet the sire, although sometimes this isn't possible. Look at the pedigrees and gain health test results for as many generations as you can. Ask yourself the question, are you happy with the breeder and the dam, is everything open and honest, can you imagine keeping in touch with the breeder throughout your new dogs life, do you think they will be happy to take the puppy back for any reason throughout its life, would you turn to them for advice?
If you can answer yes to the majority of those questions, then I would choose that breeder even if it means the litter will have a slightly higher COI.