Hehe, it does if it's on an orbital platform!

But yes, there is hardware, of course there is. That being said, there's very little evidence that physical work was even needed; as mentioned, the only reference I can find is Orbital DKs statements from Storm Front.
Since we don't know the physical hardware that "is" the Matrix, nor how these new protocols were implemented, any reference to modern day upgrades is moot; at this point, we're both just speculating wildly, really, and either of us could be more or less accurate.
2 years to develop and implement a global software update on the infrastructure owned by the Big 10 (and probably every subsidiary and supporter of the Corporate Court, and any corp with CEOs/Board of Directors that dream of becoming a member) would have worked towards this together; this represents a significant and concentrated effort as far as I am concerned. I don't think it needs to be sloppy work at all, though their goals to secure the Matrix were, as I stated earlier, largely ineffective.
To my mind, the Matrix revamp reads like the various DRM implementations that have been attempted in the modern day. How many times have we read that "We're releasing Software X with a completely unbeatable DRM system!" in a company press statement, and one day before official release the pirated version is out there?
That's what happened to my mind, which is ironic since GOD pretty much allowed the best hackers in the world to beta test their new system...