I think Johnny's arc is finished. I can't see him coming back in the expansions. But I wouldn't mind being proven wrong.
I feel like what is going to happen will be similar in structure to Witcher 3's release cycle. Johnny will be included in the mid-game DLC where you investigate some other potential lead. It's woven seamlessly into Act 2 in the same manner as Ghost Town, Automatic Love, and Down on the Street. Totally optional like Heart of Stone but it's just a fun, meaty expansion to play around in. Throw in a bunch of the free DLC and new game plus and you have content to hold people over for a long while.
Second expansion we go out with a bang: Space heist. The answer to V's neural breakdown is dangled in front of him like a carrot and Mr. Blue Eyes is holding the stick. The story is more personal now. The place is a giant resort in space. Freeside from Neuromancer. The rich-person's paradise from Elysium. Deep Space 9 on steroids.
You enter the Crystal Palace and run around a new yet relatively contained open area. Who do you run into during your search for the data? None other than Morgan Blackhand himself. He went dark after the 2023 Arasaka incident, and has been working for the NUSA. They are investigating MBE and the organization that he represents. The threat he poses extends beyond Nightcity's borders. You team up and return to Nightcity and the plot thickens. Sandra Dorsett shows up and her involvement with Nightcorp becomes more clear.
You investigate more leads in Nightcity and it becomes apparent MBE is up to no good. When his acolytes raided Arasaka for tech they forgot to mention they chucked ol' Adam Smasher into a pickup truck and hauled him out. He's got blue eyes now and he's standing between you and the answers you need. An epic fight ensues and everything goes black.
You hear a faint melody pick up but it's familiar. You've heard this tune before. You open up your eyes and you're in a cart traveling down the road to some castle. The guy next to you is gagged for some reason, and the other guy says something about storms, cloaks, and dragons - bunch of nonsense. You hear Judy's voice crackle in over the audio: "Pretty great game, huh? This guy named Todd kept porting this game around and managed to get a BD made for it."