I think it's simple. Satoshi was using a standard PC plus a custom FPGA (just doing SHA256), so the nonce incremented not very fast. He knew his rig was too fast, he needed to reduce his chance of finding a block, so that other miners could also mine bitcoins. So he left some holes in the LSB of his nonce to reduce his chance of finding blocks.

In summary, Satoshi was clever enough that he mined enough coins without being noticed that he had a powerful rig.