The answer to your question seems obvious: a larger font would make for poorer information density. I'm always surprised at how the alternative-to-HN websites that people build don't seem to get how important this is. They invariably show fewer posts per page.
My comment originally spelled out that there is a tradeoff between information density and readability, but then I deleted that part as obvious. Anyhow, the point is that HN's font sizes, as well as much of the rest of its design, are clearly an attempt to balance those two values.
