can't answer you about the small cell. don't use it. however, on your super, chances are they will hatch out that brood and backfill the space with honey. even if they don't, as they reduce in size, you can take that super and harvest the honey later. good thought about the small cell causing them to lay drone brood in the super. i'll be interested to see how that question is answered.
as for a hive needing more than 2 deeps the answer is yes, sometimes. i don't know how long your flow lasts or how your weather goes, but this late in the year i would probably let them lay in the honey supers rather than adding another deep. for me, it would be to late. days begin to shorten and flow diminishes. brood rearing slows. can you pull some honey frames from your 2 deeps and replace with drawn frames? you can always add the honey frames back later.