Robert Rodriguez, the director, was building his house at the time of filming, so a lot of the architecture you see in the Cortez's home is in his house.
When we see the president's daughter in her room while receiving some video mail from Juni, look beside her. She has a doll that looks like Juni.
The sequence where the camera is flying over the ocean into the house is the same on from the first movie, just sped up and "hidden" with the large font of the actors' names.
If you've seen the part of "Four Rooms" called "The Misbehavers" you will notice in Spy Kids II, Antonio Banderas is combing Juni's hair and it's almost the same scene as when he combs his son's hair in Four Rooms. (same director)