Agents of SHIELD has yet to address Thanos' snap, but Spider-Man: Far From Home shows a potential way forward. Despite suggestions to the contrary, Agents of SHIELD is inextricably part of the Marvel Cinematic Universe. The ABC series has featured Samuel L. Jackson's Nick Fury and Thor's Lady Sif, and has also referenced events from movies such as Avengers, Avengers: Age of Ultron, Captain America: The Winter Soldier and Thor: The Dark World, among others. Agents of SHIELD has not yet dealt with the events of Avengers: Infinity War, and has ignored the Decimation entirely in season 6 so far.
Some have claimed that this is because Agents of SHIELD is not actually canon to the MCU, or that the show now exists within its own timeline. Given how deeply Agents of SHIELD's history is ingrained within the franchise, however, it's clear that the only reason the show has ignored Thanos' snap is because suddenly having half of the cast turn to dust is really inconvenient. Previous major events within the MCU have either been explained away with a few lines of dialogue or integrated into the plot, but there's no clear way Agents of SHIELD can do the same with the Decimation, giving how all-encompassing the event was. For this reason, it's entirely understandable why there has been no mention of Thanos in the series so far.
Nevertheless, the distinct lack of human dust within the SHIELD team remains an elephant in the room and a nagging inconsistency. Thankfully, Spider-Man: Far From Home has the ideal solution.
As the first MCU movie since Thanos was defeated, Spider-Man: Far From Home had the unenviable task of dealing with the aftermath of Avengers: Endgame and the sudden return of the 50% of people thought long dead. The movie approaches this task in a surprisingly light-hearted and inconsequential manner, referring to the infamous five-year dark period as the Blip. In fact, the events of Avengers: Infinity War have nowhere near as much bearing on Spider-Man: Far From Home's story as many might have expected.
There are references to people displaced after coming back to life, with Aunt May holding a rally for those struggling, the excellent student-made introduction video highlights how some of the class are now younger than they should be and Flash attempts to use the situation to his advantage by legally purchasing some in-flight booze. And that's more or less it. The core Spider-Man story is barely changed by the events of the previous two Avengers movies; Peter is still chasing MJ, his friends all have the same dynamic and his relationship with Aunt May remains endearingly close. Only the death of Tony Stark truly impacts the story of Spider-Man: Far From Home and, aside from that tragic loss, the setup is only superficially different from that of Spider-Man: Homecoming in 2017.
Agents of SHIELD could pull the exact same trick between seasons 6 and 7, or possibly even following a mid-season break. When the current Shrike arc is finished, Agents of SHIELD could return with a five year time skip, picking up the action after everyone has returned. Agents would be discussing the Blip, Iron Man would be a figure of legend and SHIELD might have spent the intervening years working on the ground to help those affected. As far as the audience is concerned, however, very little would've changed. There would be the same SHIELD team, still protecting Earth from extraordinary threats, only some characters would be five years older - hardly enough of a gap to require recasting.
This would allow Agents of SHIELD to address Thanos' snap without having to make wholesale changes to the composition of the show and, like Spider-Man: Far From Home, the characters could pick up more or less where they left off. Alternatively, the Decimation could help create interesting new stories and character relationships. For instance, what would happen if Fitz blipped and Simmons didn't?
Rightfully, Avengers: Infinity War felt like a seismic shift in the MCU landscape but, as Spider-Man: Far From Home proved, that doesn't necessarily have to be the case moving forward, and if Agents of SHIELD has been avoiding the issue for this reason, a solution needn't be as complicated as many might assume.
Agents of SHIELD season 6 continues with "Collision Course Pt. 2" July 12th on ABC.