Ever since using a decent anti-virus I've NEVER had anything come and hurt my computer. I've had trojans try and do something, but my Internet security just wipes them clean. Funnily enough after one of my old XP installs as soon as I went on the internet to get software to protect my PC I came across a trojan.
If I had to do an emergency reinstall of windows, if I wasn't a sensible user, then replacing a video game activation would be the least of my worries. A game is replaceable, my files, however, are not.
The only issue I have with these activations is that if I understand correctly, they rely on the internet, whilst, yes, only a small percentage of people can't get access to the internet, the problem is if they shut down their servers for any reason. Though I suppose the argument for that is if that does happen, it'll be so far down the line that there'd be a work-around for retro-gamers.