They can estimate mass based on an objects size, distance, and by how much light is bent by gravity. Finding an average of mass contained in an average volume allows for an estimate. Dark energy is not considered in this estimate because it is only responsible for the acceleration of the expansion of the universe. It works against gravity in spreading out mass, so we can assume it doesn't contribute to mass in anyway.
Well, duh, the obviously can't. Astronomers have made a guess of the size of the universe, and that means that the mass is guessed. For all we know, the universe is infinite. It's impossible to know the size or mass.
Frankly, I don't know. And so does nobody else yet. We are still working hard to chart what we see as "the universe", and only 1% or so is covered so far. There are to many unknown factors still to make statements about the mass or size, and a number of other things. The real science elite in that field don't deny that. But if people want to make calculations - paper is patient.
It's 73% and we don't know because 1) higher dimension and 2) it's there can't touch feel it etc? but dark matter is 21% it's has no mass but gravity weird isn't it and you can calculate the mass but you have do exponential numbers in thousands for stars planets galaxies and asteroids every atom of dust nebulas etc?