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I will speak about the N64 CIC chip, which is the latest one Nintendo
designed, and with which I have some experience. the N64 CIC in the
game cartidges acts as a key, and the N64 PIF chip found inside the
N64 console acts as a lock. When the N64 is powered on, a small BIOS
stored in the PIF chip is executed and reads the 1st 1kb of the
inserted game cartidge. It then does some checksum over the data using
a custom algorithm. The resulting value of this algorithm is a 48bit
number. This 48bit number is then sent to the CIC, and if it's not the
value it expects, it locks the console.

This is a protection so that people can't temper with the 1st 1kb of
ROM of the game cartidges, for security reasons. But this is not the
only feature of the N64 CIC. During the gameplay there is constant
communication between the PIF (which is also an ASIC btw) and the CIC,
and if it fails the console is locked aswell.

That is for N64 but the same mechanism is surely true for NES and
SNES. To sum up, you can't program on a CIC chip, and you can't "read
the program" of a CIC chip, because there's simply no program, just
hardware (gates, registers, etc) with a specific function.