Dusseldorf Airport is not a very big airport. 55 minutes are well doable and the major obstacle will be the length of the non-EU passport check/immigration queue.
But I would personally not worry about it as most passengers from Japan should have an easy case, which makes the queues move quickly. You will not share the queue with EU citizens, as they have ...
You don't need to transit through Düsseldorf HBF if you want to travel from Düsseldorf Airport to Amsterdam. From The Düsseldorf Airport, you can take a train to Duisburg and proceed from there to Amsterdam. Here is an example:
For schedules and fares, you can consult the website of the German Railways (available in many languages). You will see that there ...
Using the Website of Deutsche Bahn you can check the trains. There are about 350 trains a day, so you won't have to wait a lot.
But notice that there are 2 train stations at the airport: one for S-Bahn line 11 (Bahnhof Düsseldorf Flughafen Terminal) and another for all the other trains (Bahnhof Düsseldorf Flughafen).
A single ticket costs 2.40 EUR, a ...
According to a comment by @simbaque:
I asked at the Lufthansa check in booth at TXL. They said the airline takes you to a special holding room until the international connection is ready. I joked that it's probably a dark room in the basement. He said it is in the basement indeed. The police is not involved at all.
I'm posting an answer since I don't have enough reputation to comment DCTLib's answer. His luggage won't be sent straight to the flight to Hamburg. If I'm not mistaken, he is taking Eurowings from Dusseldorf to Hamburg, which means that this flight is independent of the flight from Tokyo to Dusseldorf since low-cost carriers mostly don't offer transfers. He ...
40 minutes could be enough but it could become scarce. As your second leg is a domestic Schengen flight, you will need to get through security and passport check. With only 40 minutes between the flights it's likely to miss the flight to Munich.
I was just there 3 weeks ago and had no issues connecting to my flight to Napoli. The 3 terminals are connected and you can get from one to the other quite easily. Since you only have a hand luggage and an EU citizen, 60 min is more than enough. Since it's on a single ticket, they know you're coming to and connecting to a flight, so do not worry.
On www.gratisparken.de you can find a lot of free parking places in and around Düsseldorf. The closest to the airport are on these streets:
And on www.duesseldorf.de there is also a map with all official P&R in Düsseldorf.
You first take the train to Düsseldorf Hbf (main station). It is a 5 to 10 minutes ride (depending on the number of stops) and there are some 6 to 8 trains/hour.
From there, you can either walk about 10 minutes to your hotel or take the 709 or 719 tram to the "Berliner Allee" stop and walk from there.
Taking a taxi from the airport to the hotel is of ...
If all your flights are booked on the same ticket, this means that the minimum connection time for this connection is met (unless your travel agent circumvented some rules, which they normally not do).
Passport checks in Dusseldorf are usually quite quick. Please keep the comments to your original post in mind - you will need a "proper" Schengen visa for ...
If your first flight won't be delayed, two hours are enough time for a connection in Düsseldorf. (You can cross it from Terminal A to Terminal C in less than 15 minutes).
As for your luggage - you have to ask your airline.
Here is the information about flight transfers at the Düsseldorf airport: Transferring.