Using CM7 there really shouldn't be any need to boot into Nook stock unless you want to. What I found was best was transferring any books on Nook stock to the Nook app on the android side, thus never needing to boot into nook stock ever again. That being said, No, the nook stock side cannot see the CM7 side and vice versa. You cannot share directly either direction.
Regarding Kindle and Overdrive, what are you trying to accomplish? I can probably help if you could be more specific. If you want Overdrive to find books on the Nook side, it's not possible and, I think, not desireable. Use the Overdrive app on the android side and just get books through the app. I know it's a really odd concept to purchase a Nook and then not use it as a Nook, but as I'm sure you've realized with CM7, you can do nearly EVERYTHING you can think of on the android side...except see the nook side