Out here in the desert, sunroots tend to grow in the wild in meadow areas that are just slightly dryer than what cattails like. I'd guess that the top of a hugel might be drier than their preferred habitat, so they might not grow all that robustly.
I have sunroot weed patches in my fields. I can kill them fairly easily if I pull them after the plants are about a foot tall, and before they start making new rhizomes. They don't travel around the garden, they pretty much stay where they got planted.
I think if you harvest heavily every season you should be able to keep the sunchokes somewhat under control. Just plant them in a sort of out of the way spot where they won't cause too much trouble and go for it. Worse comes to worse you can always just put a hot compost heap over the top of em and call it a day!