There are a number of ways of approaching not only this topic but also the topic of Deity in general. Often Deity is perceived as an archetype and within the Jungian school of thought, the "dark" Goddess therefore is representative of our "shadow" self. One book about working with the Dark Goddess in this concept is "Mysteries of the Dark Moon: The Healing Power of the Dark Goddess" by Demetra George (1992). In this book not only are various "dark" Goddess myths are examined - those belonging to Llith, Medusa, Kali, Morgana etc - but how to use these myths to understand our own "shadow" self .. that part of us which we reject, ignore and which, as George points out, is not necessarily a perceived "negative" trait either as what is rejected can also very well be a talent that we do not want to acknowledge or accept out of fear and/or ridicle ...
My personal perception of Deity is that they very much present - and not just an archetype. This does not mean, however, that I do not use the sacred myths and legends as anyone else would in the sense of providing guidence and lore - for I do. However, and I can only talk from personal experience, Deity is very much alive, living and breathing, touching and caressing .. and all this is reflected in the perfect balance that is all around us in the natural world.
Why we tend to lable things, Deity or otherwise, is an individual thing. The word "dark" for an extremely long period of time has come to relate to something "negative", unpleasant, even "evil" - whereas "light" is positive, nice and pure. In the West these stereotypes surround us all the time and are so deeply engrained in us, that it can be nerve-wracking to investigate the truth behind the lables.
Dark Goddesses themselves fall into a number of catagories. The more common one is that of the "Crone" or the aged wise hag. However, for Goddesses such as Pele, Lilith and even Morgan le Faye, "hag" hardly seems appropriate. Even the Goddess Hekate is who often referred to as a "Crone", has been worshipped in various guises, many of which appear to more closely resemble a "Maiden". Likewise the Hindu Goddess Kali-Ma is often actually referred to as "Dark Mother" by Her followers.