Only thing I don't get is why the T-800 would not know what crying was and need to have it explained why it happens. If he has detailed files on the human anatomy why wouldn't he know about tear ducts and why wouldn't he be familiar with the concept of emotional distress?
His neutral net processor (learning computer) is set to read only by skynet, so he can mimic and "learn" on a limited basis, but he's essentially a parrot, with no real understanding of what it is to be human. So even though he has detailed files of the human anatomy, that information is there to primarily make a more efficient killer. His knowledge and understanding is very limited.
I guess after the T 800 is "killed" by the T-1000, and he's forced to use the alternate power cell, he finally has access to understanding emotional distress, and why he says, "I know why you cry." He's self-aware, understands emotions and what causes the tears beyond a physical level, but he unlike John, has no way of crying. He could probably mimic it tho in the read only setting.
When he first asked John, "What's wrong with your eyes?", he probably asked him because he knows humans have a gland that produces tears, but only on a basic physical level. And since John was no hurt physically, he was curious as to why his eyes looked that way. Joh later tries to explain to the T 800 the same thing, but he still didn't get it beyond the physical/human anatomy.