Are you using R2014a or later? In this version, Model Explorer gained the ability to search through referenced models. If you look at the screenshot below, there's that Search in referenced models option.
If you're using an older version of Simulink, just make sure all your referenced models are open (or loaded in memory) so they show up in Model Explorer. Then, search the Simulink Root instead of the top model. This will search through all your open models, i.e., all the ones that show up in that list.
