Maybe they don't have an unlimited budget for bandwidth charges? I'd strongly recommend they go behind a (free or cheap) caching CDN first before removing limits.
Also, the rate limiting is probably meant to be based upon the client's IP, not the proxy IP. Usually, the proxy adds the client IPs to the request headers and you can use those in Nginx rules.
EDIT: boosted again...gosh, HN front page is no joke :D
EDIT 2: I ran into multiple rate limits, some of which were harder to discover/configure than others. Site should be back again. Sorry.