Why do I have to buy the same items twice?
Solution 1:
Every time you can purchase an item multiple times, it is an upgrade and the bonuses are cumulative. The Awesomenauts Wiki shows these levels under each ability's tech trees. The bonuses it lists are the total bonuses at that level.
Here, each time Spiked Tongue Piercing is available for purchase in game, it will list +3 Damage.
As mentioned, once you have maxed out a particular upgrade, it will become green in the shop.