I also mostly use d3 for its powerful helper functions nowadays: scales and axes, colors, svg path generation, geographic projections, array functions like d3.group (formerly d3.nest), csv/tsv parsing etc.

I tend to leave DOM manipulation to Vue.js unless I need to animate transitions between states. I find it easier to reason about binding data to an html/svg template with Vue than to mess with d3 data joins and enter/update/exit pattern.

d3 is and stays an impressive piece of work.