yes you're right about where to get them, and it's because their nature of being a collectible item, that's why you can find them mostly when buying some goods or during some events ^^ usually every Miku event in Japan has a Sonoca card in the goods list, not only Magical Mirai, Miku Symphony and Snow Miku, but also the various Sakura Miku events, 39culture, pop up stores, etc.. ^^
you can find them also on Amazon JP or Yahoo auctions, and also in some local stores (especially in Akiba) and Animate
collecting cards is popular in Japan: years ago there were thousands of different phone cards to collect, and then companies started to put different designs also on the pre-charged cards (like for Playstation Network and train). In fact, there are various Miku themed phone cards, train cards, PSN cards, credit cards, Club SEGA cards, .. ^u^