I'd double up the plywood.
I had the same situation in my living room. I tore up my carpet to install hardwood on my subfloor. The builder used rally crappy materials. I think some of the plywood may have even been 'used' when it was installed. They also used small scraps to patch the floors rather than using larger pieces. I found several 16" x 12" pieces of plywood on the floors in my bedroom. It barely spanned 1 set of joists. When you stepped in that area, you felt the board flexing.
The floors bounced and squeaked like crazy. I bought 3/4" plywood, glued and screwed it over the old flooring. I made sure to hit the joists with 3" deck screws, and made sure that my seams didn't line up with the old seams.
When I was done, that floor was incredibly solid, and no more squeaks.