When was the last time you were there? I went in 2019 and 2020 and it was really easy to get around. All stations have signage in English almost everywhere. Google maps says which exit / entrance to come in or leave from, even which car of the train you're on is closest to the path you need to get off.
As for walking, you don't need to walk _everywhere_ but it really is cool to spend a few hours like OP said and just walk around your hotels neighborhood or other places.
I usually stay in Higashi Shinjuku when I visit, and if I hadn't done that I wouldn't have known about this really quiet residential area that leads to a nice quiet park. Or the little Korea town neighborhood that's about a twenty minute walk away.
Pre-Google Maps, finding specific addresses could be a bit challenging--because of the addressing scheme that I've not totally grokked to this day--but even then I don't recall the subway system being a particular challenge relative to other big systems like New York or London.
Don't worry. You're not the only one. Natives are often lost. Couple of times already I've been asked where the given address is by Japanese person and I am definitely not of Asian descent :) On the contrary, in 2008, before the mobile Internet I was looking for an address and couple of natives couldn't find it despite the fact I got address and a picture printed at hand. Turned out we've standing next to the building and all I had to do is to turn back to find it. Today I just follow uncle Google advice.
At least as of a few years ago, a lot of the Google Maps UI/feature work was done out of the Google Tokyo office, so it tends to be really useful there.
As for walking, you don't need to walk _everywhere_ but it really is cool to spend a few hours like OP said and just walk around your hotels neighborhood or other places.
I usually stay in Higashi Shinjuku when I visit, and if I hadn't done that I wouldn't have known about this really quiet residential area that leads to a nice quiet park. Or the little Korea town neighborhood that's about a twenty minute walk away.