I often use
Inkscape with a support grid for diagramming. You can create your own preferred square or axonometric grids (for hexes or triangles), and they are saved along the Inkscape original file; they're part of the document properties.
My own workflow is such that I often use tools like
Graphviz and others to generate an initial diagram or graph from text format data (lists of nodes and edges/connections); then I look at it a bit, and redraw it in a nicer form. During the redrawing my mind wanders all about inside the structural design, and I often get ideas on how to improve the structure I'm diagramming.
While that works very well for me, it may not work well for everyone, of course.