$100s have plenty of commercial value. Any time you're exchanging physical things of high value, cash is key. Cashiers checks, etc., can and are forged. Also, gamblers regularly walk around with 10s of thousands of dollars on them.
That's one thing I like about Danish money; the 500 kr note (~$90) and 200 kr note (~$35) are both common and regularly used. Makes it much more convenient to use cash for things like groceries or restaurants without having to carry around a thick wallet full of wads of $20s. Sure, many people use cards too, but you don't have to if you prefer cash.
The greatly increased CoL in Denmark also somewhat necessitates the prevalence of larger denominations.
I don't find much difference in CoL between the Bay Area and Copenhagen. If anything it's slightly cheaper in Denmark (more expensive restaurants, but cheaper rent). If you're comparing median U.S. CoL, sure, but even in high-CoL areas like San Francisco and New York City, $100 bills seem rare, despite the fact that >$100 tabs at NYC restaurants are not exactly rare. The difference seems to be that Americans are wary of larger amounts of cash, so use a card for anything nontrivial (or among older people, a personal check), while Danes can go either way, depending on personal preference. I'd blame it on the difference in mugging rates, probably.