Yes, they're still up and running.
That Pirates one would have been brand new when y'all were there. I recommend doing this one at night because so many of the props/stunts have cool lighting elements that can't be seen during the day. Fewer crowds too, since waiting in line to activate a prop is lame.
The Phineas and Ferb one was originally a Kim Possible-themed game, but was re-themed and slightly upgraded.
There's actually a neat homage to the previous scavenger games hidden in Adventureland among the pirate props.
There was also a small Muppets Most Wanted interactive hunting game last spring at EPCOT. It wasn't as elaborate as the Kim Possible/Platypus hunt, but it involved some neat puzzle elements.
It's not a scavenger hunt per se, but at Animal Kingdom they have the Wilderness Explorer program.