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The best answer here is composed to three points:
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When you book a room in Germany, with either one of the large websites like booking.com, Expedia or similar, you will be able to select your arrival. Most places will honour that. If you book direct with them, write down and ask for late check-in. If that doesn't work either, give them a call and explain you will arrive late.
I travel on Friday evening a lot, and have arrived after 10pm in many German cities. This has never been a problem as long as the hotel reception is still open. When I lived in a hotel for several months in central Berlin I would often talk to the evening staff, and they would sometimes complain that not everyone has arrived yet, leaving a check-in for the night watchman rather the actual trained hotel staff.
It has never even occurred to me that a hotel would give away your room if you don't show up early. There's a comment on the question that says this is common, but I strongly disagree. I've not seen this, and in fact business hotel websites even advertise that you can cancel up to 6pm as a feature of their service.
You cannot usually leave your credit card number with a hotel in Germany. That is exceptionally uncommon, and if a hotel would ask that of me, it'd be a massive red flag. Of course you can do a payment guarantee through a website, but never over the phone in Germany.