Travel photography in Japan is as simple as ABC, it will Always Be Crowded. Don't let that deter you as it is a marvelous country and an unforgettable experience. When traveling with family, photography is secondary to the shared adventure and memories, so quick response to photographic opportunities is best and accepting that you'll miss some "keepers" is part of the bargain. Still, when properly prepared you will come back with some very satisfying images.
On our recent trip, I carried the Nikon Z7ii with the 24-200mm and 14-30mm, being quite pleased with the coverage and results. We used public transportation exclusively so light and compact were essential. I would not carry anything larger than that kit, and APS-C would be a smart choice as well. When visiting shrines and temples, you will frequently be in your socks, so wear warm ones and be prepared to photograph while carrying your shoes in a plastic bag. As much as I dislike a camera strap, it was a lifesaver too many times. In many museums, you will need to check your camera bag in a locker, so a large pocket or two will come in handy. Keep in mind that, many times, photographing the most iconic locations with deities, Buddhas, and other statuary is forbidden. I am not a religious person at all, but these are places of reverence and worship and are to be respected. They are beautiful, sometimes exquisitely so, and my best advice is to turn off your camera and enjoy the serenity and calm that can be achieved even in a crowded atmosphere. You will find yourself adjusting ISO frequently from native up to 3200 and keep your shutter speed in a range that your image stabilization can handle. Just remember to check them after you leave the shrine :)
Here are a few tips that will make your trip easier. Before leaving be sure to go to the Visit Japan website and fill out the entry data. The QR code will make entry a smoother process. We used the Welcome Suica card for all of our public transportation (the bullet train does not accept any IC cards, however). Japan is a cash country in many respects. All shrines and temples are cash entry and many of the smaller businesses, restaurants and even a few taxis are cash only. ATMs are everywhere, so getting cash is easy. Download the GO Taxi app. It is so smooth and taxi fares are very reasonable. You will walk a lot and comfortable shoes are a must. So, if you are finally exhausted or the bus schedule is too complicated, take a taxi! Super important, go as early as you can wherever you can. You won't be alone, but it can make a huge difference which you will notice most when you are leaving the location.
Finally, learn lots of phrases. I memorized about four pages of travel/restaurant/direction/politeness phrases and it made a huge difference. 30 minutes a day for a few weeks and you'll be there. The Japanese speak very little English and in the rural areas sometimes none at all. And really, should not be expected to. You can get by with gesture and Google Translate, but if you make the effort, it is much easier, they will appreciate the effort and respond in kind. More importantly, you will have some simple, but delightful conversations!
Japan is beautiful, exciting, extremely polite, steeped in tradition and ceremony, and a truly wonderful place to be.
Enjoy.