"if it ain't broke, don't fix it."
A "super computer in a shoebox" is NOT needed by most functions. in fact, the only place where super speed and super-computational power is needed is ON THE GROUND, crunching numbers sent back from things like the Mars Rovers or Saturn Probes.
Since COST is a very very real hardship to NASA (seeing as how President Obama is cutting the funding almost to nothing, and the space program is about to die), it is MUCH better to get things done with CHEAPER, older technology than with newer and MORE EXPENSIVE technology.
you also have the cost factor of re-usability and volume discounts for purchasing. OLD computer technology can re-use OLD software, while NEW technology requires NEW software to make full use of the new features. that means you haev to PAY SOMEONE to learn the new software, and THAT costs money, too.
i found out many years ago that we sent to the moon using computers that used CORE MEMORY. Now, Core Memory is about as ancient and slow as you can get. ALL computers now-a-days use Integrated Circuit memory, which is fast and cheap.
But Core Memory has one VERY important feature that IC memory does not: Core Memory is NOT susceptible to radiation! While IC memory is fast and cheap, it can also be damaged by radiation in space! Now, even one BIT being off in the Flight Computer would make the difference between them getting home, and them missing the earth and flying off into interstellar space.
So, while IC Memory was cheap and fast, Core Memory was used because it could not be damaged by radiation.
It took another 20 years before Radiation Hardened (Rad Hard) memory chips were available for use is space-going devices.