It's totally in HT's business model/corporate DNA. Hot Topic's business model is about commodifying, accessorizing, and packaging subcultures in order to sell them at a huge markup.

ThinkGeek conveniently packaged nerd/geek culture as a set of things you could buy. Delightfully nerdy things, sure, and their employees seemed to genuinely be pretty nerdy but the model is not too different from HT. Now that being a nerd/geek is starting to become 'cool' (see recent uptick in portrayals of geeky/nerdy protagonists in non-comedy hollywood, etc.), HT probably wants to package up nerd/geek culture, and acquiring ThinkGeek was probably the most straightforward way to do that.

Both HT and Geeknet are in the business of selling clothes and fashion accessories to popular subcultures. There may even be a bit of overlap between the two customer bases. Also with geek subculture seemingly on the rise and the HT targeted subcultures seemingly on the decline it seems like a smart move for HT to diversify.