So, what is the etymology of the phrase? The jury is out, but here's the best theory I could come up with doing a web search:
In Boston, where baked beans are famous, the phrase was used to announce when the beans had cooled down enough to enjoy. The phrase became popular in the eighties, when Bush Baked Beans had a talking dog named Duke in their commericials who used the phrase. The flaw in this theory appears to be that Duke doesn't say "Cool Beans" in the ads - his famous line is "Roll that beautiful bean footage." Odd. And anyway, why would you announce that beans served hot, were now cool? Who wants to eat cold baked beans?
A second theory is purported here:
Known to of first become common in the US during the early 1980s (mostly among teens), made up of two terms: the pre-existing cool (which became common slang earlier in the 20th century, though was based off a term from one of Chaucer's poems), and the late 20th century American teenage habit of combining slang/common words together. Hence bean (slang for head/hair) or beans (gumption, toughness, balls), was in use to say someone was cool, in a tough/good looking kind of way. And is the nature of slang it evolved and came to be associated with the actions of said individuals. Some report that it was a way of differentiating between describing someone as cool vs the action (or proposed action) as in: being 'cool with it'.
I personally have never heard anyone use the word 'beans' to describe a person's toughness, but you can make up your own mind.
Now I feel even dumber about using the expression.