"Well, because I know you mom", Simon said, after a pause. "I mean, you and I have been friends for what, ten years now? I know she gets like this sometimes. She'll think better of it".
Clary picked a hot pepper off her plate and nibbed the edge meditatively. "Do you, thought?" She said. "Know her, I mean? I sometimes wonder if anyone does"
My educated guess, I mean, my hunch is:
"Do you, thought?"
Do you (?) - referring to "I know she gets like this sometimes."
Thought - I assume this "thought" is short for something like "you think you thought", that is, about something that the first character thought her/him knew about "she" (indicating perhaps misgivings about the event "she´ll think better of it".)
Sometimes they don´t use plain English, one has to dig under the seemingly obscure wording! That´s it. Indeed it would be easier it were two sentences, but sometimes it´s a colloquial context, and sometimes it´s about author style.