With such an ominous title, Heart of Darkness delivers what it promises: ruminations on the nature of evil. 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 takeover of peoples and land outside of the European continent mostly during the 15th through 20th centuries). So yes, 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" – the black native Africans – who reside there, practicing certain non-European customs such as cannibalism.
But why is the African jungle called "dark"? The easy answer is there’s not a lot of light in the jungle, what with the thick foliage and unpredictable fog. The complicated answer is that, according to the novel, the wilderness hinders men’s senses and renders them metaphorically blind to their situation and surroundings. The heart of darkness also suggests a confused and unenlightened state of mind, a state of profound madness where one cannot do good but one can only choose the lesser of a series of evils.