How to conceal the underside of roof sheathing with protruding roofing nails

I wouldn't worry too much about it. The plywood is not typically supporting a load of more than the paper and asphalt shingles that were placed, even more so if you have a considerable pitch on your roof to where it would be difficult or impossible for a person to walk on. It basically serves so that you have something to nail the shingles down securely.

Most newer homes use plywood, I have an older home that used what looks like rough cut deck planks and those are mostly still original. The last time I had my roof replaced, they had to change out a few boards that were terribly dry rotted and some that were badly damaged from previous water damage by the oh-so responsible homeowners who had the home before me. Other older boards look noticeably damaged by the most recent nails but they continue to hold down the shingles and I would still feel safe to stand on my roof.

As long as the shingles are doing their job then the plywood will not be exposed to any water, and as long as your attic has good ventilation during the summer time then you should have nothing to worry about for the next 15-20 years at least.

The plywood of your roof is typically not as thick as your standard galvanized steel roofing nail, so it is expected for nails to show through this in your attic. The plywood can and is expected to take a bit of damage over time and this is okay as long as the shingle has something firm to hold itself down onto.

Over time if the plywood is too damaged to properly hold down new shingles or becomes too dangerous to walk on safely then a roofer should be able to identify such compromised plywood board and replace it as needed.

What is worrying about your question is that you specified that the roofing nails have split and damaged the roof trusses. Standard roofing nails should not be long or thick enough to split or crack structurally sound dimensional lumber.

If this is what happened then you may have a problem unrelated to the quality of the roofing job. Your home is over 50 years old in a warm wet climate, so you should inspect for a number of different problems.

1. Dryrot

2. Termites

3. Carpenter Ants

If you have any of the following indications of current or past damage to any of the three items then that would explain split, cracked or damaged roof trusses during a typical roofing job.

On another note: The soffit typically fits into a groove that is known as J Channel when installed on a roof overhang. The roof overhang is typically MUCH too tall for any roofing nails to reach soffit. I imagine instead you might be seeing a roofing nails perforating the fascia, which can be a sign of a sloppy rushed job. Without pictures though we can't tell that for sure.