How large are you envisioning your game board being? I’ve played around with a few hex games in the past, and have actually tried both approaches. I would highly suggest a simple 2D array.
If you go with a simple 2D array approach, you can still think of it as a square grid, but offset the y coordinate when the x coordinate is odd while rendering. Internally, you can think of pulling the rows apart vertically then shifting the odd columns half their distance to the left.
The reference approach is definitely neat, but it creates a lot of headache in generating the nodes and references. Just my two cents, but I’m curious to hear more.
Best of luck!