Quite a few bike cylinders have holes either cast or drilled into the bottom of the cylinder. If it looks like the holes are there for no reason, there called lightening holes. All they do is lighten the engine up a little bit. It there's holes on the cases and they match the cylinder, they are most likely water jackets. The only purpose for holes in castings or machined parts are to reduce mass, to make the overall weight of the bike lighter to make it faster.
