The last three children’s movies that I have seen (all released within the past year or so) all referenced aliens. And this is not including "Chicken Little" which is explicitly about alien contact.
The movies are: Open Season, The Ant Bully, and Happy Feet.
Of these three, Happy Feet went furthest into it as a plot point. One bird explicitly talks about how he was abducted by aliens and tagged. He tells a detailed story – it is not just a passing reference.
Numerous times, the humans are referred to as aliens. “They are intelligent. They are the ones who are causing the shortage of fish." (The main animals in the movie are penguins).
I think that Happy feet is quite well done as a movie. In my opinion, two of the main themes echo two of the major events that may be currently happening on this planet - human/alien contact and environmental degradation. While one could argue that these events have been happening for thousands of years, what is different now is that they are coming into general human awareness.
While there have been alien references in children’s movies in the past (say 30 years), I think that the incidence is increasing. And lately, particularly in animated children’s movies, at least for the one’s that I have seen, it seems that it is more common to have at least one or two alien references as opposed to no alien references.