Translation:Why is she crying?
Actually, as interpreted by the ancient Chinese character dictionary, 说文解字, the radicals/components included are two mouths (not two eyes!): 口口 "to speak loudly" plus 獄, simplified to 犬 (which is an old form of 狗, 'dog'), which may have been a phonetic indication of pronunciation, but also implies a dog's bark, or perhaps two dogs barking at each other. There are a few different interpretations, but with loud talking and dogs barking, it implies that there's a lot of noise going on - enough noise to make one cry, perhaps? :-)
Although I can see where you're coming from, those are not two eyes at the top (that would be 目目) with a teardrop coming from them; the "teardrop" is part of the character 犬. So, in this case, it's just a coincidence.
I'm native speaker. ”在” This character is abreviation from “正在” which implies "the motion ur doing at the moment". The difference between these two sentences： 她為什麼(正)在哭 Why is she crying? 她為什麼哭 This sentence is more complicated but more used in conversation. It could be: 1.她為什麼（在）哭 2.她為什麼哭（了） It depends on the conversation.
'在哭' is a commonly-used character combination which means "to be in a state of crying," and this is what I've heard Chinese people say when a person is crying: 他在哭。 I'm not a native speaker, so I can't say for certain whether you can say this sentence without the 在 or not: 她为什么哭? We'd need a native speaker to confirm that.
It is possible. We can say 她为什么哭?.
We are asking what caused her to cry.
为什么她在哭? is asking what caused the state that she is crying.
There's no material difference in meaning.
It is not necessarily Now because we can't tell the time from this Chinese sentence without more context.