At the time I hadn't done the hints in the crystal ball, and besides, not everybody uses hints (I myself try to avoid them as much as possible) and I think the game should still have a clear structure regardless of your playstyle.
The think button should be usable during all times of the day, showing different text depending on the stage of the quest.
I think moskyx was absolutely right about this being helpful when you're doing several quests at the same time. In 0.4, for example, you will be able to do the Main Story, Holly's, and Myrtle's quests simultaneously (if you're a new player), and having three 'think' quests in different locations should help remind you what you're supposed to do.
Visiting Rose after collecting the Moonberries shouldn't remove them from your bag. I just tried it, and couldn't replicate this issue. Could you tell me what device you're playing on and whether you're using the original game or not?