I must say I dislike how that will probably be handled
Yes, Luffy will eventually learn about Koby's disappearance, but he should have learned from when Robin was reading out the news to everyone last chapter. Luffy told her to inform him only about the most important things, but we 1.) saw that Koby's kidnapping case was already in the papers at the end of 1059 (plus a few weeks have passed too after that until the current present), and 2.) Robin knows that Luffy knows Koby from post-Water 7 (Garp's visit to the crew with Koby and Helmeppo), so is it not important to know about this, in Robin's judgment? I assume this will be another thing never really addressed, just Luffy being in shock once he hears about it from someone, but no one questioning why this info didn't reach Luffy sooner.