Is the rate limit per API key, or per IP address sending the request? If it's counted by API key (which it sounds like it is), then the comments should stop working after 60 site visitors in an hour... But, if that's the case, wouldn't the influx of visitors from HN have already broken it?
It's per IP so if the loading is done in a distributed fashion, say via AJAX, it'll work fine.
I'm not aware of rate limits for individual repos. I think they can set it up if they want but it's not enabled by default. I remember a package manager hammering GitHub with anonymous requests that they limited but that was a special case.
