If outer space is almost empty then how spacecraft can calculate its speed & number of miles it has traveled?

The interesting point is that, at the scale of the universe, a speed can only be relative to something else. What will it be? If starting from the earth, perhaps a speed relative to the earth is interesting. For that purpose, as Bob writes, accelerometers or rather, an inertia navigation system (INS) as used in aircraft, is what would be used.

But then, that will be, relative to the earth when the spacecraft started because, after a while, the earth will change its relative speed as it orbits the sun. But there is more to it!

If you move over great distances in the universe, how would you define a straight line? The path of your inertia? The path of the light? But we know that both are affected by gravity. Then your speed will be subject to time dilation. Your clock won't be the same as a clock on earth. And a speed is relative to time. How would you measure it?

Internal instruments to measure its acceleration (known as accelerometers) are one way- this can then be used to back-calculate how fast its going and how far.

Alternatively, by sending out radio signals of known frequency, this allows receiver stations on Earth to determine how fast it is moving and where it is.

The spacecraft does not know, the ground computers know.

Initial telemetry, tracking it's transmission - all worked out on the ground.

You are asking, I think, what is the reference point from which to measure and the answer is they just pick something. The speed is relative to what they chose.

trigonometry and calculus