The fact that the beams are cracked may be a huge problem, or it may be of no consequence whatsoever. Wood is a natural material, and it cracks and checks as it dries. Minor cracks are just fine. Major cracks are a huge deal. But after 50 years, I suspect any problems would have played out by now. I assume the cracks are old, and when you examine them closely, you will see that they are the same color as the surrounding exposed wood. If they are fresh, they will be brighter in color. Are the beams sagging or deflected? If not, I bet they are fine.
I notice you haven't mentioned anything about the piers. Are they sound? Have they settled at all?
A sub floor with rot in it may be a big deal, or may not. How much rot? A few square inches by an old leaking toilet that was fixed decades ago? Or a leaky roof that is still actively leaking and rotting out large sections?
Have you crawled under there and looked at it? Or are you relying on just the foundation company?
It's easy to get overwhelmed by something like this and throw a lot of money and effort at it, but there may be nothing wrong here other than some cosmetic cracks and a repair company trying to make some serious money.
Once you get some specific information, like the width of the cracks, and the dimension and span of the beams, you can go to Taunton's Fine Homebuilding
website onto the
Breaktime forum there. Pose your questions with as much detail as you can, and you will get good information.