Well the throwout bearing sounds like it is on the way out, it is part of the slave cylinder.
When you push the clutch pedal in the slave cylinder expands and the throwout bearing is pushed against the flexplate(which is spinning at engine RPMs), this relaxes the grip of the flexplate that sandwiches the clutch plate against the flywheel, so clutch plate(attached to transmission input shaft) can now spin at a different RPM than the engine, so you can shift gears or stop.
If there is a noise when clutch pedal is pushed in it is almost always the throwout bearing, could be pilot bearing but doesn't really matter since you change that when ever you change the clutch.
You also have a leak since the reservoir ran dry.
Master cylinders don't usually wear out, but that wouldn't be part of a noise issue in any case, they are not to expensive, under $50 usually.
You do want a self-adjusting Flexplate if you decide to replace clutch system.
And never get a "racing clutch disc", they are made of softer material to get "sticky" when warned up, which is great for racing but truly sucks when you have to replace it every year.