You're right, they do hide their pain very well and very effectively. If they have a condition then it is far better to just presume that it is causing them pain if it is a problem that would cause a person pain and medicate appropriately.
If the rabbit develops something new then teeth grinding, lack of appetite, lack of poo, lack of drinking, etc, and basically any other odd behaviour from your rabbit can indicate pain.
For example, cystitis pain may show with straining, not settling to a position, pressing the back end down, lifting the tail up, walking funny, etc. Pains caused by other things will show in different ways.
Basically, with a potentially new pain it comes down to knowing your bunny and reading the signs, but with an ongoing condition think if it would hurt you and then base it on that.
