The Display/Don't Display Junk option setting controls the displaying. The problem is that the trash can is always displayed.
In previous betas the junk option handling was in the Searching option, but I think the current place in Filters is much better, and for me suggests that the filtering happens not in the search time but at displaying. It would be nice to place the Display/Don't Display Junk option to the search result too and one could change it on/off even after the end of search.
Slow reply exp, sorry.