Illustration notes are fine in moderation, and you don't need to mention them in a query. However, they should be limited only to what's necessary to understand the story. For instance, you wouldn't want to add an illustration note saying that Justin has green eyes and brown hair (unless it's absolutely critical to the plot). Those sorts of details are the illustrator's job.
In the example you gave, if the words:
"Justin tripped on a stick. Hmmm? Buster loves sticks. He loves chewing on them and tossing them in the air. Justin had an idea."
...are actually in the text of the book, I wouldn't put in an illustration note for that. The illustrator will figure out the best way to show it, whether it's a thought cloud or something entirely different that you haven't even considered. :-)
An example of a place where you *would* want to use an illustration note is somewhere that the text of the book doesn't adequately convey the action. For instance:
"Fiddlesticks!" Justin yelled. [Illustration note: Justin trips over a stick.]
...a note there is ok, because you need Justin to trip over the stick, but you aren't telling us about it in the text.