If you open all the flowers, the endless spawning of heartless stop. The flowers also turn color of the magic you use.
As a side note these are not necessarily to use during the mini boss fight to free Jane and Turk. Just wail on the fruit. The flowers can be activated at any point to stop the endless spawning.
As far as I know every puzzled in KH1 had a point. Whether or not it was worth it to do is dependent upon the person and their skill level. For instance, it might be worth it to someone to do during boss fight if they don’t have the skill to balance killing the fruit and the heartless at the same time. Might also be worth it for someone to do if they want to explore that area (small as it may be) without intrusion from the heartless.