I loved her like certain dark things are to be loved, in between shadow and soul.
Can someone explain this?
What dark things are being talked about?
I'd really like to see the full text of your translation. It differs from the two translations I posted in the body of your question. In the latter cases, they use the English "obscured", but yours uses the literal translation of "darkness".
Looking at the etymology of obscure, the direct use of the English term, as opposed to the literal translation is apropos, and could be more what Neruda intended--Romance languages are much closer to Latin roots than English.
My recollection is that "shadow" (sombra) appears not infrequently in Neruda. I get a very Jungian sense of shadow in the poem, and in Neruda in general--he was certainly writing in a period when Jung loomed large in literature.
Neruda is making the point that he doesn't love the object of desire in such concrete, if poetic, ways, or love her the for obvious things. "o flecha de claveles que propagan el fuego" (arrow of carnations that propagate fire) is a reference to Cupid's arrow and the more conventional gift of flowers that inspires romantic love [See: Symbolism of Carnations]
"Dark" is surely meant in terms of obscure, abstract, difficult to quantify or qualify. He loves her for reasons he can't explain. The idea that "I love you without knowing how, or when, or from where" is liberating, because it does not require rationale or justification.
For a referent on osucra = obscure, see Cet Obscur Objet du Désir/Ese Oscuro Objeto del Deseo/That Obscure Object of Desire (Buñuel, 1977) (Essentially, oscura means oscura, and literal darkness is metaphoric only--literally it is inability to see something clearly, which can include darkness as the cause, but not exclusively. So the translation to "dark" is likely based on idiom.)
There's also the idea that loving for concrete reasons may be somewhat artificial. But real love is not bound by symbols or convention.
For a sense of Neruda's admiration of the more obscure aspect, one might look at one of my personal favorites: Tus Pies (aka Your Feet). Here he writes a wonderful love poem, made more remarkable for the non-standard choice of feature to praise.
This is consistent with Whitman's invocation in Song of Myself: "Welcome is every organ and attribute of me, and of any one hearty and clean. Not an inch nor a particle of an inch is vile, and none shall be less familiar than the rest."
After reading the whole poem here is what I understood ( I understood this poem as a man writing about a woman).
I don’t love you as if you were a rose of salt, topaz,
He began by saying He doesn't love her because she is pretty to the eyes.
I love you as certain dark things are to be loved,
When he says dark things,he might have meant that she is unusual. She is something not everyone can understand. It might also mean that she is something which can't be acknowledged openly!
in between shadow and soul
When he loved her openly, it remained in the shadows. His love for her was limited to the shadows and his soul.