I think it feels hacky because it is, and it's natural. And by natural I mean this is how spontaneous complex systems evolve. Internet is a result of half of a century of millions of people's contributions for different and often opposing goals and priorities. For other examples of hackiness take a look at other complex natural processes, like multicellular living creatures and ecosystem in general.
But Is hackiness how we humans want to do engineering? I don't think that biological systems are considered ideal models for building bridges or planes. Is software different?
I thought we were talking about what we already have, not what we want to have?
EDIT: Bridges and planes are built by strictly organized companies, with clear (ideally) leadership and plans. Internet has evolved much less centralized, and as a result, in a more natural fashion. No one stopping you from attempting to write a perfect software, but if you want to re-use results of million man-years of development, you'll have to deal with natural processes.
