Yes, they also meet Race. But ever since that, they never used the real character names. Jonny became "Action Johnny," Race became "Red" and Dr. Zin became "Dr. Z." No explanation has been given for it that I know of.
Maybe. That, or it was out of respect for the creators. I never quite considered Jonny Quest for kids, though. It was a prime time show, for one. But I understand that toons in the 60s did things that would never get by BS&P today and make oversensitive parents or "advocates" looking for money/publicity scream (i.e., 10 year-old boys with real, non-laser guns using them alongside the adults to fend off a crocodile attack). The 80s and 90s reboots were definitely more for kids, though.
A really good JQ parody that's somewhere in between was Toby Danger, which was supposed to be a stand-alone short, but was cut down into a segment of Freakazoid!. And it featured 3 out of 4 of the principal voice actors from the 80s revival of JQ.
Here's what happened: Jonny Quest has been in a state of almost being revived and yet not quite for about... a decade. This started while season 2 of The Venture Bros was being made. Cartoon Network was worried that using the same characters in a straight adaptation and a parody would damage the Jonny Quest brand, so the Quest characters on Venture Bros were renamed. The revival fell through again, but the names sort of stuck.
At any rate, as of the Halloween special, Dean knows the truth, although finding that out contributed in part to Dean going through his own rebellious phase, he started resisting his father's urgings to go into Super-Science and started dressing in a black jumpsuit and generally acted in a way that lead ol' Uncle Hatred to worry that Dean was cutting himself.