In "The Practitioner's Guide to Graph Data", the author avoid the term "node/nodes" and only use vertex/vertices and they explain it as below:
...because we are focusing on distributed graphs, and nodes has different meanings in distributed systems, graph theory and computer science.
In distributed systems, a node can be a client, server or peer, while in computer network it can be a computer or a modem. In computer science, as you already point out, it could be used either for graph theory or tree system.
So in the context of graph theory, node and vertex are used interchangeable. But if you would like to make it clear and avoid any misunderstanding, vertex/vertices is the way to go.