They're not really the same thing or a diametrically opposed choice. Vanilla is/has a naturally occurring scent, and vanilla orchids/flowers legitimately smell like vanilla. Why do vanilla flowers smell like vanilla? Evolutionary botonists might know, but I'd guess it's probably some natural evolutionary process that helps the flower avoid pests and be reproduced by pollenating creatures attracted to the scent. Chocolate is a cooked/manufactured process, you don't get "chocolate" without ... removing the cacao seeds from the plant/fruit (which don't smell like chocolate), aging them, fermenting them (which smells foul btw), cooking them (usually smells foul), mixing them with sugar and butter, etc. Vanilla, as a scent, has existed for, I dunno, let's say a billion years and our lizard scent glands evolved around the same time. What we understand as chocolate has been around since like 1850, and most people in the candle-buying world might have only been exposed to the scent, for, say, the last 80-100 years.
Most scented items tend to be manufactured around naturally occurring scents... Go to the supermarket and look at all of the scented detergent, you're going to find a ton of lavender and lemon, but not a lot of pizza scented detergent. Does that mean people like to eat lavender more than pizza? Nah. It's just that one is a relatively common scent found in nature, perhaps associated with cleanliness (like the acidity of a lemon), and one is a delicious food, but not something commonly associated with fresh clothes. Cinnamon, sage, other popular scents, I think they follow this rationale.
There's still plenty of hokey scents, but they tend not to be the most popular ones. Who knows truly why but if I'm taking a stab at it it's because our human biological/chemical/physiological scent detectors have been honed over millions of years to find scents like vanilla, sage, lavender, etc for some evolutionary relevant reason, while chocolate has really only been around for 150 years and doesn't have the same pull on your brain chemistry.
Also vanilla flavored things > chocolate flavored things 🤷‍♂️