regardless when you go, here some suggestions for cycling in Japan (Kansai mainly, as it seems this will be your main target area).
For general planning, please have a look here: http://bicycletraveljapan.blogspot.com/search/label/Planning/
you can select each region.
For Kansai specifically last time I was in Osaka I came across a cycling route map and added all the links here: http://bicycletraveljapan.blogspot.com/2019/11/cycling-routes-in-kansa...
The pages are in Japanese, but just click on the links inside and maps will open (note there are multiple links in there, some will actually lead you to Questionnaires or other useless stuff... but it just takes a little bit of clicking around and you'll find all the maps)
From my own experience, I would say riding around Lake Biwa (I haven't done the full circle though) and riding in Nara prefecture were the absolute highlights of cycling in Japan. (well, maybe the ABSOLUTE highlight is the Shimanami Kaido. http://bicycletraveljapan.blogspot.com/2017/11/part-10-day-48-49-ridin...
But that is kind of an "isolated" pleasure. While Otsu - Kyoto - Nara - Nara prefecture can all be easily connected.
I know that around lake Otsu there are bicycle rental shops. E.g. one at Maibara station, renting out more high end bicycles. In other areas, e.g. Nara at the station there are mamachari rental stations. But it seems that in this region cycling gets more and more common, so more and more cycling rental shops open. Just search for "自転車 レンタル ＆ Name of the city" and you should find some suggestions. Have a look at their pics and you can see if it is Mamacharis or better bikes.
Under this link you can see cycling tours I already did in Nara prefecture: http://bicycletraveljapan.blogspot.com/search/label/Nara
Here in Shiga: http://bicycletraveljapan.blogspot.com/search/label/Shiga
If you decide to visit now, Miho museum with the sakura blooming was stunning. Per their web page, they plan to open on 14th March... however I would be somewhat surprised if they really open. I guess that if they are closed, you cannot see the sakura either. http://www.miho.or.jp/news/%e2%89%aa%e9%87%8d%e8%a6%81%e3%81%aa%e3%81%...
and here in Kyoto: http://bicycletraveljapan.blogspot.com/search/label/Kyoto
I have made a good number of rides in these regions already, so just click through them to find something that inspires you.
If you have some specific questions about cycling in Japan or routes, let me know.
I cannot advise you if it currently is a good idea to come to Japan or not. Actually everything here is very quiet and orderly. So I do not feel threatened. It kind of "helps" that the government doesn't do a lot of testing... so numbers are low. However also the number of deaths so far is very low (compared to e.g. Italy). If you come now, however be prepared that most museums, indoor events (Kabuki...) will be closed. Outdoor sightseeing in general should be fine, and even much less crowded than normally as there are just so much less tourists around. I would advise however to check for each place you plan to visit on their web page if they are really open, as even some outdoor places have closed.
If you decide now, registering in the list of Germans in Japan (https://japan.diplo.de/ja-de/service/15-Elefand
) might be a good idea... well, at least that's what a friend of mine who works at the embassy told me... so I dutifully registered and now get relatively useless emails from the embassy...
You should make sure you have health insurance for Japan. It does not cost a lot... but would really help (financially).
Enjoy your trip to Japan, whenever it will be.