Gosh, there is so much to this simple post! The work is not making sense and the prices are crazy!
If the floor joists need to be replaced, then you can sister them or put in new ones from below. That si simple and easy. I have had a few houses that required this in TN. My two kids have been able to sister joists since they were maybe 14. The thing you also need to check is that the rim joist is in good shape. IT it the one that goes around the other floor joists and hold them together. IT is much harder to replace. My two kids could do 6 regular floor joists in a few hours, its not hard. That should not be expensive, nails, framing gun, wood, nothing special here. Could be done with the tenant in place, but why wait? Simple and fast repair.
Now, the subfloor is another thing. That can not be done from underneath. Saying the floors are in good condition is meaningless because you will be pulling the floor out to put the subfloor on those joists and then the floor goes on top of the subfloor. You can not put the subfloor on top of the joists from below. The hard part of putting in the subfloor is removing the old floor. If you are keeping the old floor it is even more time consuming. Again, not a high skill task, my teens do it, have on 2 houses so far. Its not their favorite job though, hard on the knees. If you are putting back in hardwood, that will be an expensive move. The cost of hardwood floors is a lot in the labor, each piece cut and nailed in, on your knees! This job would require taking everything off the floor, so best done with an empty house. And you can walk on the floors to see if they have 'give'. If so, I'd replace the floor before renting because it is easy to fall through, and a big liability. I personally fell through a floor on one of my houses and went straight down 4 feet. Pretty banged up for a month. And I hire people to put in the hardwood, paid $8k for a huge living room, dining room and large master bedroom, included sanding to get a perfect leveled floor and final coating.
Ductwork, I think you need to get another opinion Most of my houses have the ductwork under the house. You can get auto open vents in the crawl space, a dehumidifier, vent one of those ducts to the crawl space to put in conditioned air, wrap the ducts, insulate them. Lots of much cheaper things to do that will fix the problem.
Now for encapsulating the crawl space. Get a quote from a pest control company that you get a yearly spraying contract with. They are by far the cheapest where I invest to do this because they like to crawl on the plastic instead of the dirt. I once, for my personal house, got 2 quotes from heavily advertised companies that do crawl space work for their business, both at $5k. The pest control guy did it for $300. Yes, less than 10%. So not a use the small pest control company for that work.
But do use your quote to negotiate.