How does the Hadith: «Wondrous is the affair of the believer, for there is good for him in every affair of his» accord with the legality of Istikhara?

The meaning of "all the believer's affairs are good" is not that ease and hardship are equal. Rather, it means that the believer is grateful during ease and patient during hardship, while also striving for what benefits him and seeking well-being. This is why Istikhara (prayer for guidance) and supplication have been legislated.