One possibility is the "brick wall" technique, which uses a square grid with each row offset by half a square from the upper and lower rows. It's topologically the same as a hex grid, but easier to use in some ways.
You can always have hexagon and vertex data items, connected with pointers or references, but that might not meet your scaling requirements, and it's going to be harder to put them on a screen.
If I remember the rules correctly, it's very important to know which hexagons a vertex is on, and very important to know which vertices are adjacent to which, and most of the other relations are unimportant (aside from the hex sides that have ports or whatever you call those exchange things).
