This example i made with another 3rd party Hex grid app and also paint.net, i wasn't about to set it to single or just double digits. In your map generator, you could make an option to have the number show top or center or bottom of a hex.
Maybe also have font color for Hex number and size as options too, bigger font number might make it more readable.
And the user could turn off (if its possible) the little 1-6 table denoting POI locations to make it easier to read hex numbers. As they could easily export a version of the map with out hex/numbers and have the 1-6 legend table denoting the POI so the map is not obscured in anyway. The hex version could be for movement only.
I hope the example helps.