You're right that most web apps aren't actually "IO bound" per se. They aren't making optimal or maximal use of either network or disk IO.

However the important point is that they aren't CPU bound either. Most are "user acquisition bound" (like tens of requests per second peak). Some are more like "developer time bound" (cutting the server farm in half is not worth the cost in dev time).

Either way, using a slow development framework (including language, DB, etc.) that the developers like is a reasonable choice for what they're trying to do. (I personally wish most software was faster, but they have no reason to care what I think.)