Putting a side brake-pad materials, quality of the pads, etc...rate of wear is more dependent on driving style than it is on mileage. If you are heavy on the brakes and constant braker, then, irrespective of the mileage, the pads are going to wear off.
Having said that I do have to side with @Hyaenidae on this. It does seem like an awful lot of niggles for a 6 year old Honda. Especially with such a low mileage and what seems to be a cared for car as well. I wonder if the non-1000cc Civics are also having the same level of niggles come up (and I mean actual issues and not the whole "known to", "possibly can" situations which every engine on the planet has but actual things that do happen). I suppose it is a case of "gone are the good old days".