In "The Storm," it seems that Calixta, Alcee and Clarisse are happy at the end, but why are Bibi and Bobinot happy?
You are right in identifying that "the storm" of passion that overcame Alcee and Calixta, both metaphorically and literally, has had a positive effect on all concerned. To see how this effect has been beneficial for Calixta's husband and son, you need to examine the end of the third section of this great short story. Bobinot and Bibi are shown to re-enter their home with unease, expecting to be told off because of their appearance and the dirt that has covered them. However, Calixta greets them with affection:
She had clasped Bibi and was kissing him effusively. Bobinot's explanations and apologies which he had been composing all along the way, died on his lips as Calixta felt him to see if he were dry, and seemed to express nothing but satisfaction at their safe return.
Calixta's release of passion, much like the release of a storm in summer, has cleared the air and allowed her to return to the role of being a loving wife and mother. The sexual release that her rendezvous with Alcee gave her has been beneficial for all concerned, including, ironically, her husband and son.