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Those holes are called Su if the stone is quality it should not affect the edge. By the way none of the stamps on the stone say it is nakayama.

Have you honed on the stone after lapping? If the edges are good then nothing to worry about.

Maruka stamps are always on the side of the stone, never on top. No real maruka is stamped on top or bottom of the stone.
For a quality Jnat you should be looking to buy from someone that actually...