Is there any way that cookie clicker could have been farming CPU cycles? I remember playing it and thinking that it was consuming an awful lot of resources after a while...
But never attribute to malice that which can be adequately explained by incompetence.
I seriously doubt that. It's not just "inefficient", it's completely useless for bitcoin mining. It's something like spending $1000 in electricity to make a cent or two. It's not even worth the time to hack.
If you had that much cpu power under your control, you'd make more just selling it on darknet for 1% of its cost.