"It is a glass without water."
Translation:Es un vaso sin agua.
The difference is the use of "ser" vs "estar". In English, the verb "to be" can refer to both a temporary condition of an object, and to intrinsic values. Take the sentence "the apple is green": This could both mean that the apple is unripe (a temporary condition), or that the apple is actually the color green (a permanent characteristic).
In Spanish, the verb "estar" is used generally for temporary conditions, and "ser" is used for permanent characteristics. The usage is not always intuitive by these guidelines, though, and in this case it might be hard to tell that "ser" is the correct translation of "to be".
It is dropped. You only add a subject if it is not an impersonal sentence (like it is raining). Try to work out who 'it' is in each sentence, and if you can't (such as this one), then conjugate as 3rd person and without subject. In English it is mandatory to have subjects, adding the dummy 'it' if required, but not in Spanish.
"lo" is only used as the direct object, so while "lo" translates as "it", you can't use "lo" to mean "it" in all cases. In cases where you want to something along the lines of "it is...", you drop the subject ("it") and simply say "es...". So in this case, you would say "es un vaso/una copa sin agua." This only applies when the subject is "it" because Spanish has no pronoun for "it", only for "he/she/they".