Going to be installing solid pacific mahogany in a 12x15 2nd floor bedroom. About 3 feet of the bedroom actually overhangs the first floor. Most of the floor has a moisture content between 8.5-9.5% but On the exterior wall where there is the 3 foot overhang (front porch underneath it) the moisture content reads 10-12.5% ( higher reading right close to the exterior wall).

I am in upstate New York. Is this range going to be an issue? There is some staining on the plywood (5/8th Cdx) in this area that appears to be old moisture issues ( condensation from a huge window that beaded water off it during the winter it was so inefficient). Am I better off adding another 1/2 of Cdx or is this moisture range not a concern?

There may still be a moisture/water penetration issue where the window is. Since there is no flooring in place except for the sub-floor, now would be a good time to spray with a hose the outside of the window to see if there is any leaking.
Since you will be fastening the wood down with either staples or nails you will be penetrating the moisture barrier. There is a reason why the different levels of moisture content vary. I suppose the framing has been boxed in below the sub-floor.

I'll take a closer look. It's weird cause the drywall and the insulation that I can see at the bottom show no signs of moisture so I wonder if maybe someone just spilled something and the old thick shag carpet kept the moisture in.

Regardless I am going to add 3/8th or 1/2 Cdx or bc plywood to the existing subfloor. Can I just glue this and use a pneumatic stapler to put 1" staples to secure the extra underlayment? Last house I did I screwed the underlayment on and it took absolutely forever.