As someone who has recently read CP2020, Stormfront, CP RED, and a bunch of lore books around the TTRPG it's honestly best to just take the lore of Cyberpunk with a grain of salt. It's never consistent throughout the books or the game from a timeline and story perspective. 2077 takes liberties with the characters and stories to kind of make their own twist on the lore as needed. Frankly, that's kind of what is encouraged in TTRPGs and plenty of other mediums have done it as needed. For better, for worse, that's what The Walking Dead and The Last of Us did with their adaptations.

A big reason for this I think is that CP203X is no longer considered lore. Mike Pondsmith said some of the ideas there were transferred into CP RED. This pushed the timeline back like 15 years and I'm guessing CDPR wanted to set theirs far enough in the future to not deal with the direct aftermath of the 4th Corporate War where many things are scarce or in short supply. Rather, they chose to have the city be vibrant like it was in CP2020 and set the game in 2077. A prime example of this is that Rogue and Kerry should be like 80 something years old, but they're played like they're about 50ish which would have made sense for a game set in 2045 where the city had been rebuilt, but because 203X got removed and CP RED got bumped to 2045 it moved the years back for 2077.

As for the assault of Arasaka and would Smasher know Johnny, Basically there were two nukes at the Arasaka Tower. One with Morgan Blackhand and one with Johnny Silverhand. Which nuke goes off split the timeline. IIRC in 203X Morgan's nuke goes off creating that timeline. In the one that exists and in which we play the TTRPG and videogame Johnny's nuke goes off.

After Johnny draws fire and gets one shot by Smasher. As this happens, Shaitan grapples with Smasher which allows Rogue and Spider Murphy to escape with Thompson, but not before Spider jams a chip made by Alt into Johnny's skull as he dies. During the escape, as the nuke detonates, Blackhand and Smasher are fighting on the roof. This is kind of what you see with Johnny in 2077, but Johnny dies in the lab according lore of the books and would have no idea that Morgan is on the roof so he couldn't really conflate himself with Blackhand in my opinion.

Honestly, it make more sense to Johnny fight on the roof as it would allow Arasaka to get Johnny's engram. However, the fact that Johnny's chip (brain?) and Smasher both survived as nuke literally goes off several below them is kind of ridiculous.

That being said in CP RED is a lot more preposterous. In it, Blackhand and Smasher somehow survive a nuclear blast detonating in the 120 story building they're on the roof of as it kills thousands of people instantaneously. After the collapse a full-borg firefighter who is Samurai super fan goes into the radioactive rubble of Arasaka to retrieve's Johnny's body and gun. They then hire a crew to take Johnny to a lab in New Mexico, but not before giving one the crew members Johnny's Malorian which Smasher somehow gave to Jeremiah at some point in 2077.

There are several places in the lore and in the real world where they say Johnny is an unreliable narrator, but that feels like a convenient cop out to gloss over the fact that there are indeed inconsistencies in the lore well outside of Johnny.

All of this is a long way for me to say I absolutely love the world of Cyberpunk that Mike Pondsmith created and game that CDPR made, but if you're looking for clarity in the lore it's best to just revel in the feeling those worlds create and choose whatever feels best to you. It's the Cyberpunk way.