Well, I'm not sure it was piwik anymore. I finally had time to start digging into it and he got all my website on that host. The most likely suspect is one of my wordpress installs. Probably a bad plugin. Meh.
I was thinking search engine spider traffic... after all, traffic I get from the search engines shouldn't show the name of the search engine in the user-agent would they, I don't think?
The code he base64'd just returned (at the time) an empty hidden div, which would have been added at the end of my pages. Though I can't imagine what he would possibly want to do with spider traffic. And I still haven't figured out what he exploited. Meh.
So it was a false alarm for piwik. But if you use a crap-load of plugins on your wordpress sites you might want to do periodic checks.