Just like the Market sells items you can make, the Armory sells equipment (weapons and armor) that you can make yourself. The Market will remain relevant for as long as you are playing the game, but the Armory will become outdated very quickly, never progressing beyond the absolute basic weapons and armor. You definitely won't be dropping by there very often. However, given the convoluted nature of the weapons upgrade trees, you might be buying a few of the basic forms of the weapons you like because many weapons are only available through upgrade.
Otherwise it's a fairly irrelevant store.