Denmark has had passport checks on the Swedish and German land/sea borders for some time now. I have been waived through in a car twice in each direction (both times with Danish plates and heading to/from Germany over land and sea, but most recently, last week, I crossed into Denmark from Germany by train and we stopped for about 20 minutes while border police came though the train at Padborg.
I think most sizeable European airports can deal with shifting demand much like the aforementioned French airport, or at a push, data can be shared from around the EU with arrival countries before flights land, meaning anyone who shouldn't be traveling can get apprehended on arrival.