How can a User be in more than one room? Isn't that just a property on the User? And if you index that why would you also need to store it on the Room?
There is no one right way, it really depends on how many of each object you have and if it's a small number (as rooms and users implies) you may be better with a simpler and more robust (cannot store impossible values) approach like having a single property on a user RoomId
. That's never going to be inconsistent and if you need to find the set of users in a given room it's a cheap query.
In MongoDB you CAN denormalize the data and store an array on each object containing part or all of the other object, but you can also create an effective join collection if you want to.
For example you could have a collection {UserId, RoomId, DateTimeEntered, DateTimeLeft} with appropriate indexes which allows you to quickly find all the users in a given room at a given time. Once you have the set of Ids you could go load them if you need them for display OR you could add the fields you need for display to this table {UserId, UserName, ...} BUT then you have the problem of maintaining that data if it ever changes OR keeping it intact if you need to know that when they entered the room that's what it was called.
There are also a TON of other questions on StackOverflow relating to how you should store related data, I suggest you go read those also.