With such an ominous title, Heart of Darkness delivers what it promises: ruminations on the nature of evil. (You know, just like Wicked, but without the song-and-dance.) The "heart of darkness" refers not only to a physical location (inside Africa), but also to a state of mind and the grim consequences of imperialism (the European world takeover during the 15th through 20th centuries).
So yeah, Conrad was into metaphors. The text considers the deep jungle of Africa as the heart of darkness both for its untamed and hostile wilderness and for its supposed "savages" who hang out there practicing certain non-European customs such as cannibalism.
But why is the African jungle called "dark"?
The no-duh answer is that there's not much light in there, what with the heavy foliage and the mists. The more complicated answer is that, according to the novel, the wilderness makes men metaphorically blind to their situation and surroundings. In the heart of darkness, you can't do good: you can only choose to be less evil.