Are pads that are marked NC (No Connect) available for any purpose, such as for registers or for manufacturing purposes?
No, these pads/IOBs are not available for any use. For example, in the Virtex-II FF1517 pinout sheet, there are NCs for the XC2V4000 of the FF1517, and they are connected for the XC2V6000. There are more IOBs for the XC2V6000; as a result, there are no connects for the smaller device. When you open up that device in the FPGA Editor, you will see that they do not even exist.