It's possible, but I highly doubt it. More likely it's done using ToonBoom for instance. And a graphics program like Photoshop for the backgrounds.
General notice: from now on, I would like to ask everyone to put [AS2] or [AS3] (corresponding to the version of actionscript you are using on your project) in front of their post titles when the question is actionscript related! Please help us help you faster. Thank you.
So, I checked with a friend-in-the-know about one of the studios handling Aqua Teen, and the answer is, Yes—Flash, as well as After Effects, are used.
Just remember, and this may go without saying, but, the software is just a tool. People tend to think that if something looks simple, it must be Flash, but it's about the artist behind the tool. For instance, a lot of my students all thought South Park was done in Flash, but it's not. What do they use to create SP? Maya