I think this will be fine assuming you have the proper documents for entry (the German long-term "D" visa is listed as an exception allowing you to enter / transit through the Netherlands according to IATA TravelCentre) and regarding Covid regulations (I haven't checked these for your specific situation).
I've arrived at Schiphol (as my final destination) from a non-safe country outside the EU a few weeks ago; I think I can give you some information on what to expect. Before disembarking the plane, we were told to have our passports and Covid tests ready. As soon as we disembarked the plane there were some marechaussees who glanced over our passports and Covid related documents. This all went pretty fast, and I don't think you'll have trouble here when you have your documents ready and complete.
After that, you can go straight to the transfer section (I assume there will be a security check after which you go through passport control). I recall walking past that and there were no queues, just an employee asking if anyone had a transfer flight. This gives me the impression that while there may be some extra checks related to Covid, the lack of queues (because passenger numbers are down by a lot) allow you to go to your connecting flight without delay.
There are also plenty of employees around the transfer / passport control area who seemed to be bored by the low passenger volume. If you feel you're having to wait too long or if you're close to your scheduled departure time (within 45 minutes?), you could wave to them and say that you've got a short connection. If you have your ticket ready and you are running late, they'll probably help you move along past the queue.
I asked KLM they said that no problem. however, I really am not sure for this. If delayed what happened or if took more than expected? The next flight is 18 hours later which is really boring.
If that really bothers you then I think you could opt to leave Schiphol (assuming you meet the criteria to enter the Netherlands, which are a bit stricter than the criteria for transiting only) and take the train from Schiphol to Berlin (no direct connections). Since you have no checked-in luggage, you wouldn't have to worry about that. You just have to check if your Covid documents allow you to enter Germany via train as well (e.g. is the time of taking / issuing of your test still within the regulations set by Germany considering the new timetable).
In any case, this is more of a backup plan if you were put on a later flight with a really long wait. If everything goes according to plan then you won't have to worry about this. If it puts your mind at ease then it might be worth looking at the train schedule and doing a bit of research on how to buy tickets for that journey at Schiphol's train station.