Iresearched those two holes are traditionally for the kogai and kogatana, which fit into slots in the saya. The holes are asymmetrical because the tools are asymmetrical. They exist so that the tools can be removed without drawing the sword. (the handle for the kogatana is refered to as the kozuka, and so the hole can be referred to as the kozuka ana, rather than a kogatana-ana /end useless trivia)
Some tsuba only have a hole for the kogatana
Poorya