Fairly early on in development the decision was made that this was going to be a young DC universe, where the heroes haven't been around that long. Once that decision was made, producer Greg Weisman decided to use Dick Grayson and Wally West as Robin and Kid Flash because he felt that rather than be a strict adaptation of the comic Young Justice, which used Tim Drake and Bart Allen, they were really working with an entire history and legacy which were critical to the story.
Aqualad/Kaldur'ahm was created for this series. Geoff Johns and Ivan Reis liked the character so much that they subsequently adapted him for the DC comic books (with dreadlocked hair and the alter ego Jackson Hyde) debuting in Brightest Day #4.
One of the deciding factors on how the producers chose the main characters (Robin, Aqualad, Kid Flash, Superboy, Miss Martian and Artemis) is that they wanted to have adults that the kids viewed as mentors or as parental figures.
Lead character designer Phil Bourassa and producer Brandon Vietti made a conscious decision to try to handle the Justice League with a little more of a classic design sensibility than the Young Justice team. They did this to try to visually show the difference between generations since the series is all about that dynamic.
The Producers went into this series with two goals: to capture the interests of not only the youngest kids but also the older crowds and to make the show feel as realistic as they could with animation.
The Young Justice team is similar to the Impossible Missions Force from "Mission: Impossible" with teenage superheroes. They operate from the abandoned Justice League cave, are supervised by the android Red Tornado, trained by Black Canary, and given their covert assignments by Batman.
There was a spin off comic based on this series. Even though it's based on the show, the creative team wanted the comic to have it's own continuity that runs alongside the series and be interesting in its own right.
It took months to have this series get the green light, because Warner Brother and Cartoon Network and DC are all part of the same Time-Warner family, so getting them to communicate with each other takes a long time. In October 2009, the series finally got the green light.
The trivia item below may give away important plot points.
In the finale of the episode Secrets, the title's namesake is revealed to be from a magic shop called Abel's House of Secrets. Fittingly, Abel's House of Secrets was the name of a mystery/horror anthology series published by DC from 1956-1978.