Hello there,
Big thanks for all four suggestions. I came back from Japan a few days ago, and as a way to give something back to the community, here are a few reflections from my search for second hand lenses in Tokyo.
First of all, Japantraveller posted a link to an excellent article from March 2018 on various second hand camera shops in Tokyo. This is a top notch source to refer to. Also, I was nicely surprised how well google search works in English for Japan.
Following the advice above, I went both to MAP Camera in Shinjuku, and to Fujiya in Nakano. Both were very good and seem to be doing most of their business trading in second hand equipment (although they had some brand new cameras and lenses too). MAP has the obvious advantage that it is located right smack in western Shinjuku, where a lot of other camera shops are located (and the Olympus showroom). Going it Nakano is a bit of a trip - but well worth it. BTW, about 50 meters from the Fujiya lens and camera shop, they have a smaller operation dealing in tripods - great choice of 2nd hand heads, legs, and other related equipment, which is not available at MAP.
I cannot comment on prices of s/h bodies, as I was not in the market for those. But when it comes to lenses, ordinary SLR lenses (say, with prices up to about 2000 Euros) were quite expensive even when second hand. As a ballpark, a s/h Canon L lens in excellent condition would cost about 20% less than a brand new item. Since photo equipment in Japan is quite expensive to start with, in my case it did not make sense to buy s/h lenses, as the price would be close to what the same item costs brand new in Europe.
However, the price was much more attractive for big primes. For example, a second hand Canon 500/4.0 mk II was available for about 5,600 Euros, while the same lens brand new costs about 10kE in Europe. So this is indeed an attractive option.
All in all, for those in the market for big primes, it may be worth to go to Japan to buy a s/h one - the price difference would cover the cost of a trip to that fascinating country, including a week's vacation :)
So there you have it. And thanks again for the helpful tips above.
Pawel