Clearly you need a better lens. The 18-55mm is extremely soft which shows even more with 24 MP sensors. Instead, if you are looking around the same focal-range, the AF-S DX 17-55mm F/2.8G is immensely better. You will get much higher resolution with it but know that optically resolution rarely is uniform. Even with a sharp lens you will have to stop down a little to get maximum performance which will minimize softness near corners.

Know that the 12 MP figure though is misleading. As I mentioned already , sharpness is not uniform. Most lenses are reasonably sharp in the center and get softer towards edges. When the aperture is stopped-down from wide-open, sharpness increases up to a point, until the diffraction limit is hit. An 18-55mm kit lens only gets sharp around F/8 to F/11 with the diffraction limit being around F/13 which does not leave much room and is very dim which increases chances of shake which adds softness.

To answer the first part of your question, it is simply the lens which is blocking sharpness. Light blurs as it enters the lens and therefore the sensor cannot record an image which has sufficient definition. You will set get a 24 MP image out but it will have details comparable to a 12 MP image according to the figure you quote. Again, this is not entirely accurate as the center could look like one taken from a 16 MP image and the corners from an 8 MP one.