I thought the same as you, I have all the items in the game, so maybe I don't need anything, I already beat the final boss, maybe that's why I'm like that, I don't think I need to beat all the roots of the dungeons for something to happen, it didn't give me a quest either
The Roots do have a mission. I believe... don't quote me on this. Somebody did tell me that. Releasing all the roots. With those big nails. I believe they told me that it powers up the strange fruit. That you get from that Lady that you can pay for 20G.
Like it makes them more effective? I'm not really sure. But I think that's what it does.