No. #fiftychat is ran on our own server by Till, and we have not had a single problem. #civfanatics, #erebus, and #nes are ran on another small server, and that server has had flood bots *very rarely*, but overall both servers seem secure.
I don't know much about this stuff, but I've heard that viruses/spyware/bots/etc. are mainly a problem on the big IRC networks. Both #fiftychat's server and #civfanatics's server are small and, in my experience, safe.