The neverending "refugee crisis" (the official reason several countries have introduced checks within the Schengen area) has allowed more frequent checks, but it seems fairly random whether or not they happen. Out of perhaps 10 overnight journeys, I've not been checked going south or east, but around half the time I've been checked going into Denmark from Germany.
It's so disruptive that I no longer take the overnight train into Denmark. You should prepare for it — put the passport in the mesh holder so you can just hand it over — but I find it difficult enough to sleep on a moving train anyway.
Having recently visited Germany via plane, they have certainly gotten stricter/performative. Leaving Munich for London and despite already have presented passports to immigration, they had police checking passports on the gangway to the aeroplane…