Your "deck" of Opportunity cards isn't a literal deck with a known order. Instead, it's a pool of cards: every time you draw, you'll get a random card from this pool of cards, except you'll never draw a card that's currently in your hand. The odds of drawing each card from this pool is weighted by its Frequency.
It has long been known that some cards are more common than others, and you'll occasionally find advice to "trim your deck" by dropping various Connections below 5 (so that you don't draw the fairly-common "conflict cards" of, say, Revolutionaries vs. Rubbery Men). Other cards, like the Recurring Dreams: Death by Water cards, are rarer, but required for some Ambitions (and also for Seeking Mr. Eaten's Name, which is a terrible idea). Personally, I'm still exploring the mid-game content, so I haven't seen a need to optimize my Opportunity deck for anything specific yet; who knows when I'll need some Connected: Rubbery Men?
I don't have any hard evidence yet for exactly what each level of Frequency means, but now that it's a publicly-displayed value, we can start looking for precise answers. (Or, more likely, imprecise answers; "Standard" frequency might mean a weight from 4 to 6, or some such.)