I use simple 2D lat lon grids for different regions and resolutions. E.g. the global grid uses 2879x1441 pixel grid. The third dimension is time. All data are stored directly as floating points on disk. Because I know the dimensions of the grid, I can read data exactly at the correct position on disk. I use Float16 as well, which saves me 50% disk space compared to Float32.
Fancy hexagons like H3 are not necessary. They could reduce storage by ~30%, but require much more effort and I have to "modify" the forecast. I keep forecast data from national weather services as untouched as possible.