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You can do that with the Pre-Selection Navigator tool (I think that's what it's called)
Place the cursor over the position, and press the up or down key on the keyboard to display the Pre-Section Navigator and Auxiliary Viewer. Scroll up or down in the list of geometry until you come to the hidden face and Enter to select it, or select the hidden face directly from the list.
To help with selecting mating features for assembly constraints, another method is to Publish the features in each part and name the features accordingly. When creating the constraint, all you have to do is select the feature in the tree for each part. This way you can apply constraints even when you can't see the part or the feature.