If the master cylinder was not empty there should not be any air in the system. When the level is low, mechanics know to never add any during other routine service such as oil changes. The level is low due either to a leak that must be addressed immediately or because the front brake pads are worn and ready to be replaced. As the pads wear down the pistons move out of the caliper housings. That is the self-adjusting feature of all disc brakes. Brake fluid leaves the master cylinder's reservoir to fill in behind the pistons. Those pistons have to be pushed back in to make room for the new, thicker pads. Doing that pushes that brake fluid back up into the reservoir. When someone fills the reservoir in between brake service intervals, that extra fluid spills over and makes a mess on the floor and it will eat paint off the body.

Whatever the reason, once the brake pedal is pushed all the way to the floor, there is a real good chance the master cylinder will be damaged. Crud and corrosion build up in the lower halves of the bores where the two pistons don't normally travel. Pressing the pedal over half way runs the lip seals over that crud and can rip them. That may not show up for a few days but it will cause a very low pedal, a slowly sinking pedal, or the inability to build fluid pressure in one or both hydraulic circuits