Why does this LED matrix have two 5V and GND pins?

Probably for better reliability - high current connections can fail over time from corrosion (especially if humid), have a backup gives a better chance of continuing function as well as reducing the current per contact.

Being conservative with ratings usually pays off for enhanced reliability.

Though it could just be that they have a standard power harness connector across a whole product range, so use the same connector on even the smaller arrays even if over-engineered…