Insects are good at...piercing...darkness? It's the only type advantage thing that makes no sense to me. I mean, even with Flying over Fighting, there's a bit of logic, sort of. Birds are probably super hard to punch. But Bug over Dark? WTF?
Nocturnal? That's a good explanation. Though, for the most part, Dark type mainly consists of street-style "dirty" fighting. So I kind of figured well, something along the lines of. . . actually I got nothing.
I think dark types represent corruption/evil (hence why they are good against psychic, aka the mind, but do little against fighting, aka the body)... bugs are not intelligent enough to understand evil. They can't be corrupted by darkness, therefore dark types have little effect on them.
Also, saying "Bwahaha, I am evil! Come to the dark side!" won't stop a bug from crawling on you or biting you. It might even get you to forget about evil for a minute, and instead think, "Holy ****, get this thing off me!" XD
In many different games, there is sometimes a point at which mechanics and story/logic don't make sense. When game developers have to decide which one to support, it is almost always better to choose mechanics.
I think this is the main reason why Bug is super effective against Dark. Without it, only Fighting would be super effective against Dark, and since Dark was created to bring down an overpowered type (Psychic), it would be hypocritical to make it overpowered. Plus, Bug was only super effective against Psychic and Grass. Dark's low amount of weaknesses met Bug's low amount of strengths and a new relationship was born.