Because

[acoustic tendon]

Squares aren’t traditional, they’re just what is used in minecraft and all other games ripped off of and inspired by minecraft.
Bitcraft definitly has inspiration from minecraft, but the reason for using hexagons is clearly not just to be different. The game mechanics and appearance all benefit from this system, using it as a base for structure positioning and terrain generation. I vaguely understand why it’s cool, but I don’t know quite enough about all that programming and game design to further elaborate.