The deal with PS3 BC is quite convoluted.
The first Japanese units, and the very first North American PS3s shipped with a PS3 "guts", as well as the PS2 "guts" (the combined EE+GS (Emotion Engine + Graphics Synthesizer) chip used in the PS2 slim). In effect, your PS3 has two consoles inside it - the PS3 Cell+RSX stuff, and a PS2 Slim.
To save costs (it was costing Sony quite a lot to make a PS3 - estimates had around $2400 or so per PS3, or roughly 30 PS3 games or many, many, many Blu-Ray movies), Sony got rid of the EE unit, instead emulating that and still having the GS. These units were first introduced with the European models, and carried back to North American and Japanese markets. These units have software emulation, and reduced compatibility.
Then Sony needed to release an even more lower cost PS3, and Sony got rid of the GS period. The lack of a GS pretty much eliminated all hope of PS2 compatibility. PSX compatibility came later, mostly because the Playstation Network Store started selling PSX games to run on the PSP. A few firmware revisions later, it became possible to play these PSX-PSP games on the PS3 - Sony wrote a fully software emulator for the PSX on the PS3. This isn't that big a feat, since the PSX is quite weak by today's standards - 33MHz MIPS R3000 CPU and a basic CPU, and only 2MB of RAM.
Unfortunately, the GS is very difficult to emulate, being a highly advanced GPU with a fully programmable core - think of it as another MIPS CPU with advanced vector units.
This is why now all PS3s can emulate a PSX, but only those with a GS can emulate a PS2. In addition, if you have an early model PS3 with the EE+GS chip, you can switch between the software emulator and hardware, by enabling/disabling the upscaling feature (I believe - I haven't verified if it uses the software emulator while upscaling is on, and the hardware while it's off).
As for cost - the less parts it takes to assemble a PS3, the cheaper it is to manufacture. Less parts to go bad, less parts reduces the chance a unit is defective during manufacture, less inventory, less heat, etc. etc. etc.
Anyhow, new PS2s are under $100, and if you're going that route, it's cheaper to go with the $400 PS3 and PS2 than the $500+ bundle, unless you want the game. And PS2 games are still coming out. Unlike the Xbox, where Microsoft laid out a timeline after which no more Xbox games will be made and basically ended Xbox games (everyone migrates to the Xbox360), the PS2 is still a money maker for Sony. Heck, Sony will probably keep making PS2s until the PS4 starts getting finalized (like they did with the PSX - that thing was still being made as the PSOne until a few years ago!).
