hoofrehab.com, barehoofcare.com naturalhorsetrim.com among others will explain & illustrate the problems that 'navicular' horses have. Basically, 'navicular syndrome' effectively means unexplained heel pain and 'navicular disease' means there is also damage to the navicular bone &/or deep flexor tendon.
It is thought that toe-first landings are a big cause, as this directs a horse's weight down onto the navicular bone, where it is unsuited to take the concussion. High, contracted heels are the usual problem. Correct trimming to encourage good hoof mechanism & growth, keeping heels/frogs in contact with the ground is a big step towards rehabilitating the horse.
Farriers & vets will sometimes advise even greater heel height and even bar shoes, preventing the frogs from having any stimulation, further weakening them and forcing toe first landings. This is because this can have a palliative effect, reducing discomfort, usually only temporarily tho. While this could not bring about rehabilitation, it was better than nothing when people didn't understand what was wrong with the whole picture.
I don't know of anything that shows holes in bone can be repaired, but some bone damage, including extra ossification & spurs around joints, can become repaired or removed when the hooves are able to function effectively. There is also plenty of evidence that suggests it doesn't really matter if the nav. bone or DFT are damaged, so long as the hoof is functioning properly. The horse can still be rehabbed back to usefulness in most cases and is not affected by the damage.