The simple reason why parts get more expensive is because high capacity storage like that is newer technology. 1GB of memory usually consists of two sticks of 512 MB. 512MB sticks have been around for a while and are easier to make, so they cost less. However, a single stick with a capacity of 1GB costs more than two 512 sticks because the 1GB stick is more convenient. With 1 stick of 1GB, you still have a second slot open for a second stick of 1GB giving you 2GB total. The same thing goes for 512 sticks, even. It's cheaper to buy two sticks of 256 than to buy one 512 -- because one 512 is more convenient. HDD capacity is sort of the same thing, high capacity HDD drives are simply more convenient and a little more complex on the inside.
As for buying upgrades, you don't need to buy memory/HDD upgrades from Apple. While I'm sure you could have Apple make the upgrades for you, there are far cheaper alternatives available online to install yourself if you have the basic knowhow.