The other hole...
Open the master cylinder back up (make sure the housing is level) and you will notice a small round tower in the center, that holds a small silver spoon looking thing. This is a deflector that covers the small hole that you are asking about.
When you remove the deflector (just held in place by three legs and friction) you will see the other hole. Note; when you replace the deflector, make sure you replacing it correctly so there is a small gap between the base of the housing and the shield. It is possible to place them back in upside down (shield flat against the floor obstructing the flow) which would not be a good thing.
I find that using a children's aspirator filled with brake fluid the perfect tool to suck and blow through both holes to clear them out.