They can charge more for a console with an 80GB drive as opposed to a 60GB drive, and the cost to Sony is marginal. They might pay an extra $10/unit, and then be able to charge an extra $100 for the entire console. Meaning they don't lose quite as much money with every console sold.
I don't buy the cost saving excuse for removing the EmotionEngine chip myself. They're still going to be cranking out PS2 units until around 2010, and every one of those needs one of those chips. So the cost savings are likely negligible. If I were to don the tin foil hat and speculate a bit... I might think it was a subtle and passive means to try and encourage people to regularly update their PS3 firmware. So if a usable exploit happens to be found in one version, the majority of people will have updated to a version without the exploit in order to get better backwards compatibility. There was also a glitch in the EmotionEngine chip that allowed most PS2 games to be run from a HDD on the older "fat" PS2s, and the early slim PSTwo models that had IDE connection points you could solder to. There might have been some fear that someone would figure out a way to adapt that to letting PS3 games to run from the console's HDD, or that someone would adapt it to the PS3 to allow the PS3 to play pirated/legal backup PS2 games. Who knows, maybe someone working for Sony figured out such a way.
One of the other posters pegged it though. Gameplay wise, every PS3 console from the first one to roll off the assembly line, to the last one to roll off the assembly line will have the same core specs regarding gameplay. Same CPU at the same clock speed, same amount of RAM, etc. If there weren't that consistency in the hardware you couldn't guarantee that games made at the end of the console's lifecycle would run acceptably on early models. If that were the case then you'd have the same mess as the PC gaming world. Every 6 months to 2 years you'd have to buy a new console to keep up with the games.
Speaking only for myself, but representing probably millions of people, that's exactly the sort of situation that drove me to console gaming. I may need to buy 1-2 consoles for a given generation. Even if I bought two PS3s at $500 each, that's $1000 spent for say 5 years worth of games. How long do you think that same $1000 would likely last me in the PC gaming world? Not even close to 5 years, that's for sure. Even the most frugal bargain hunter would probably be lucky to make it last 3 years.