How strict are room occupancy limits?
 

Traveling with Japan with my wife and our two kids (3 and 1 year old). Booked in suites mostly (Park Hyatt Tokyo, Ritz Carlton Kyoto, Aman Kyoto). All the properties I have looked at have a max room occupancy limit of 3, even if it is a 1000sqft+ suite. How strict are these limits? Do you think I will have issue staying with two kids?

Japan is per person . Usually get passports looked at at checkin. I guess you can hide other people. But committing fraud is foreign country is not a good look. I think they even tax per person

try contacting the hotel and add your kids to the reservation

Agree contact the hotels. Japanese married couples with two young children are not booking 2 rooms when staying in hotels based on my experience of travelling with my Japanese colleagues, observations and with my family, staying several hundred nights in hotels thoughout Japan.

Hotels usually have a rule about children under a certain age who don't require extra bedding (i.e., sleeping on the same bed as the parents) not counting as extra people. But for the specifics if it's not shown on the website, then better call.

3 and 1 year old you should be OK.
It's where they start hitting school age in Japan (6 going on 7) that they start getting ratty / want to charge you extra money.
But as a matter of courtesy you should tell them.

This sounds right.
Some hotels make it clear regarding children's ages, but often only via the Japanese website.

I checked the Ritz's Japanese site, and if you enter children a second box pops up and asks their ages. I put it two and it showed no availability. WIth one child it was fine.
If it were me, I wouldn't worry about it, but if you want to be safe go ahead and call.

The Ritz charges the same member flexible rate for 1 adult, 2 adults, or 2 adults plus one 3 yo.
For 3 adults there is an extra person fee.
They won't book a room for 4 persons.

Park Hyatt shows the same rate for 1 adult or for 2 adults plus 1 yo and 2 yo

Aman offers two bedroom "pavillion" rooms for 2 adults and two kiddos. The same rate, well over 2 million JPY, is available for 1 guest. I see a king room for one guest is 414,000 and 2 adults is 424,000

Anyway, you seem to have three options:
1) rebook or modify existing bookings
2) ask for what you want if it is not offered
3) FAFO

Am a big fan of option 2. If you don't ask/state what you want, then you won't get it.
(in general, a Japanese saying "that would be difficult" is saying "no")