In the circumstances of the Known World, horse breeding could be quite different. Due to the Rash threat, the horses could be kept in smaller quarters to be able to keep them protected. And horses could be extremely valuable, so you wouldn't need a herd of hundreds for it to be a source of considerable wealth. Speculation, of course.
As for the loss of breeding charts and perhaps the prize immune stallion (the ONLY immune stallion in Sweden??), it could be an economically devastating blow. Also, if Emil's father was very distant with everyone, maybe him dying in the fire would also cause a catastrophic loss of know-how, causing the business to disintegrate despite some of the animals being saved. I was also thinking that maybe there were huge hospital bills for an injured Thorolf, but I hope the Nordics have stayed true to their character and provide universal health care, such as any is available.
So yeah, I like this speculation!