There was once on a lifetime when I was in the same thing as you were. It was tedious, but it gave me much more control over stuff. I looked at the items, and there were lots of unuseful things, and unbalanced equipment. Also, since I want to do some eventing stuff that needs it to be as organized as possible... it was mandatory!
Also, think about your players. RPG Maker drops all the stuff in the same order as you have it, and players can't change it without you remaking menues (and even with that is easier to just forget about the database! haha!).
So, if player1 wants to use potion3... where was it??
So, well done!!