[fforw]

Were there ever really common peek and pokes that would change programs?

Yes, "poke 53280,0" would directly write address 0xd020 to 0x00 which then e.g. would turn the border black on the C-64. But those were addresses in the mapped custom chips. More like setting a pixel on a modern GFX card by poke and less changing a program.

The later development of expansion cartridges to give you more lives in games or enable a cheat-mode there would a kind of peeking and poking, but hardware based etc.