In the truest sense of the word, no, you cannot "upgrade" a weapon, tool, or armor aside from installing mods. However, every weapon, tool, and armor piece does have a quality level (Q1-Q6) and the higher the level, the better the stats (in general--depending on the item, things like weight or stamina usage may increase). While you cannot physically upgrade a weapon to a higher level, you can craft them based on crafting skill. You can scrap the lower quality version for parts.