Answer: Maybe and maybe. There is a possibility that the inspector should have spotted this, but you state that the repair is not visible from under the car. This would lead me to believe that the repair was either done to perfection (not likely, but possible), or the old floor pan was cut out and the new one replaced in such as manner as to be hidden by the frame when viewed from underneath. In either case, the repair would be nearly invisible and the inspector could easily miss this. However, there are telltale signs that might tip off the inspector such as fresh undercoating, new brake or fuel line sections and clamps, or evidence that the seats or sections of the exhaust had recently been removed. These bits of evidence disappear slowly over time as the newly repaired section, as well as any new parts, tend to blend in with the surrounding area. The older the repair, the harder it will be to spot.
The only sure way to reveal a repair of this nature is to remove as much of the interior as is necessary to expose the floor pans. This brings up the question of what should, and should not be expected during a pre-purchase inspection. In most cases an inspector will not do any disassembly of a vehicle. It is usually cost prohibitive, and the seller generally frowns on it. Exceptions might occur if the model of car being inspected is known to have issues that can only be discovered by disassembly, or if the buyer suspects a defect.
The value of any classic car is certainly affected by rust repair, but in your case the effect is probably minimal. The price point of a 1969 Lincoln Mark III is not high enough for a quality repair like this to have a significant negative impact on its value. On the other hand…if the repair was done poorly, that’s a whole different story.