It's a mistake for the roofers to say that the plywood will definitely have to be replaced. However, they may be familiar with homes in your area, that were built around the same time. So they may have experience, that tells them that the decking will likely have to be replaced. Sometimes in situations like this, contractors will pad the estimate with the cost of replacing the decking. When they do the work, if they don't have to replace the decking they'll remove/refund the cost.
All that being said. I don't know these contractors, and have not talked to them. I can't say for sure what their intentions are.
Comparing plywood used as subflooring, to plywood used as roof decking is a mistake. Roof decking bakes in the sun, freezes in the cold, and may be surrounded by moisture laden (potentially salty ocean) air . While the subfloor rests comfortably in conditioned space (typically).
I'd say guaranteeing that the plywood will need to be replaced, is just as wrong as assuming it won't.
If it were me, I'd bring the concerns right to the contractor. You might find that they have a rational explanation. I'd find out if they plan to simply replace the decking, or if they're going to inspect it first. I'd also ask them if they'll reduce the price, in the case that the plywood is in good shape and doesn't need replacing.