I finally found some last week at a Foodworks on Elizabeth St, in the Melb CBD. I was tipped off about them from a friend who had been in there a few days before. Asked the bloke on the counter how they had been selling and he said "extremely well". They get their orders in on a Thursday and by the Tuesday the week prior they had sold out. I think (although I didn't completely follow) that they order 6 boxes a week (12 Yowies / box = 72 Yowies). I was in the same store a couple of weeks ago and there weren't any Yowies so they must have just started stocking them. They were on the counter (see photo).
The friend that tipped me off had mentioned that the woman in front of him was initially very excited about finding them at the counter but then didn't purchase when she found out they were $3.50 (which i personally think is quite reasonable). When i bought a couple last week they were $4.00 so perhaps given the high levels of demand they increased the price.