I worked on a Smart TV project about 2 years ago. To be honest I can't really help with a prototyping tool specifically for Smart TV, but when I did this project I actually used some exiting prototyping methods.
I wish I could share some pics but the project was under an NDA . But I can tell you what I used!
- In the very early stages of design I used paper taped over the TV in the areas my app was going to overlay the broadcast. This helped me to watch a broadcast (e.g. sports game) with the areas covered by my app. I really wanted to see if the places that my overlay was going to appear would interrupt/obscure an important part of the sports match. This was really helpful before going into detailed designs. Maybe only helpful to you if you are designing an overlay app.
- Then I used a standard InVision clickable prototyping with an iPad (connected by bluetooth to the TV) as the interface instead of a remote. This doesn't help you much if your specifically looking for something that can prototype the use of the remote. But it does give you the experience of standing in front of the TV and controlling what is happening on the display.
- At later stages I worked with the developers to test basic designs over the real broadcast. But this takes more time for the developers to build. So you should only do this once you have validated some other things like positioning and general interaction with low fidelity prototypes.
I hope that helped a bit. I'm not sure if it matches your needs. But it's probably hard to find too many people working on Smart TV stuff so I thought I would add my 2 cents. Happy to talk to you 1-1 if you think it would help