Although not explicitly stated anywhere I know of, I would consider Malignant Cell to be a Death creature. It has the color borders of death creatures, and can only be created with Death Quanta and Death Cards.
Thus, I believe Darkness/Eclipse in Darkness, which state "All death or darkness creatures gain +x/+1" should apply to Malignant cells.
If the idea is to make this not happen, then Malignant cell should be changed to the color of artifacts/colorless cards so this confusion subsides. Either way, the current way seems to be a glitch/oversight.
If anyone has any thoughts, please post them.