I recall specifically reading somewhere (but I cannot find it), that the person who coined "dependence"/"dependences"/"dependence graph" purposefully avoided the word "dependency" because he felt it had negative connotations.
In any case, a directed graph that illustrates relationships such as "A depends on B" is a graph of dependence relationships. Whether you call it a dependency graph or a dependence graph, and whether you call the edges in said graph dependencies or dependences doesn't bother me. The former is more standard English, I believe, but the latter is fairly common in computer science textbooks. I try to stick to the latter when using the computer science concept, but I admit it sounds funny.