Simply reality vs. theory.
The counters on all my Nikon DSLRs are always conservative, which is good. I think that Nikon has programmed a fixed-size image for the exposures remaining estimate since each frame is slightly different when compressed and saved. My files seem to average 9.5-10 MB/file.
I shoot raw only and always get more frames per card than the counter shows. A rule of thumb for me is that 4-Gig card is about the equivalent of 10 rolls of 35mm film, 36 exposures. When I shot 4 GB cards, I usually got about 360 raw compressed images on any of my cameras. Today, shooting a 16 GB card is roughly 40 rolls equivalent--about 1400 images+.
As for batteries, using freshly-charged batteries, I'm getting probably 1000-1200 images per charge, if not more. In cold, this will be lower.
A good upgrade is to use the MBD-10 grip and both the battery in the camera for back-up and an EN-EL4a in the grip. You would then get better than 3,000 image per pair with power to spare and an extra frame per second rate with the camera on continuous.