I think that this sentence is wrong. Unfortunately I cannot report it now as I don’t know anymore in which lesson it appeared.
One can say “Estas varma tago” translated as “It is a hot day”. And one can say “Ĝi estas glaso” translated as “It is a glass”.
While “it” in the first sentence does not really refer to a thing, the word “it” in the second sentence refers to an object. (With object I don’t mean a grammatical one.)
I don't know why this was downvoted; it's a valid question.
bluematt said it first, but in short: glaso refers to the drinking vessel itself, not to its composition, which would be vitro.
Therefore, since the glass in question is a countable item, when translating this sentence into English you have to indicate the quantity, which we do here by using "a".
Officially, not often, although in general use it can be.
That would depend on context. e.g. If there was a box, and you asked "what's in the box?", someone might reply "estas glaso" (a glass exists [in the box]). If there was something here, and something there, one might say "tie estas glaso" (a glass exists yonder). These roughly translate, with emphasis, to "there IS a glass" and "THERE is a glass" respectively.
'There' is fairly ambiguous in English, not so much in Esperanto.