In Russian, words change endings (or sometimes change completely) depending on their function and meaning in the sentence. One such instance is when the is a nul quantity or absence of something. Вода (water) is a noun in the nominative case. Cases describe the way a word has been changed to serve a particular function in a sentence. You may have talked about conjugating verbs. Verbs can conjugate (depending on the language) just like in Russian, nouns change according to the conditions of their environment. This is called declension. The nominative case (naming case) often correlates to the subject of a sentence in English, but not always. The genitive case of nouns serves several functions. If I want to say "I have water" in Russian, I would say "У меня вода." There are two nouns in the Russian sentence, just like in the English version. In English the nouns are "I" and "water". At this point in your experience, you have undoubtedly seen the Russian word for "I" in the nominative case "я". If I do not have water, water must also be in the genitive case. "У меня нет воды" has two nouns in the genitive case. "Меня" is in the genitive because it is the object of the preposition "у" which means roughly "with". The "а" at the end of "вода" has changed to "ы" as it is in the genitive case.
"Кто" in Russian means "who" in the nominative case. In the genitive case, however, the word changes to "кого". "Who" is classified as an interrogative pronoun, but it's essentially a noun and as such has the characteristics of a noun including case. When the "who" part of this sentence is negated by asking "Who is absent?" or "Who isn't here?" the "who" must be in the genitive case.
It may be helpful to look at a Russian case chart. A native speaker of Russian would recognize these changes implicitly and not really rely on a chart like this.
I literally interpreted the phrase "Кого сейчас нет?" as "who is not now?" which makes no sense in English. I guessed that it meant "Who is not here now?" OR "Now, who is not here?" but wouldn't that phrase in Russian be "Сейчас кого здесь нет?" By the way, Google translates "Кого сейчас нет?" as "Who is not currently", so that's interesting... I guess in Russia this might make sense (I really don't know) but in English, not quite to me.
Нет = "не есть"
It's more like "Of whom/Whose presence is not [present] now?" if you want to get technical. Кого means "of whom" or "whose".
Also when any noun is directly negated, its case becomes genitive. Нет никого, нет яблока, нет машины, нет человека. The noun is in the nominative case when its presence is not negated. Есть кто-то, есть яблоко, есть машина, есть человек.
In Filipino, it makes total sense. Кого сейчас нет = Sino wala ngayon.
Unfortunately, English doesn’t have a single word for “нет” or “wala”, so you just express the same meaning with multiple words.
Нет = не есть = not is = not present = absent = not here
Word-for-word, the closest translation is “Who is absent now?”, but the more natural way of saying it is indeed “Who is not here now?”.
1) "Кто сейчас отсутствует"
"Кто" is a question of Nominative, so it used with words in Nominative case
2) "Кого сейчас нет"
"Нет" is a word of Genitive case, so it works witn questions of Genitive "кого"/"чего":
The source (in Russian): http://nashol.com/2011060955536/tablica-padejei-russkogo-yazika.html