I went looking for clear plastic tubes some time ago for adding rooms to Hampture. This website will sell you them in a wide variety of diameters, 'wall thickness' and length.I'll have to do precise measurements of the habitat but offhand I think a 2 inch diameter tube would give the hamster plenty of room to crawl through (he's perhaps one inch wide) and it wouldn't exceed the dimensions of the habitat wall.
My current plan is to trace the outline of the tube, pressed up against the habitat wall. Then I'll drill a pilot hole, then use bigger drill bits to gradually widen it. From there I'll use a dremel to eat away at the plastic until I've completely cleared out the interior of the traced circle with as much precision as possible. Perhaps leaving a slight "rim" near the back so the tube has something to be mounted against. Then comes the gorilla glue for a firm hold, and the marine sealant around the edge.
I think I can afford the tubes, but I'll need a dremel tool and set of appropriate tips. I'm pretty confident this will work perfectly, and before long we'll have a multi-enclosure habitat.