I think Sony only pulled out of E3 this year because they don't have any major game announcements left for this generation. Also, E3 isn't cheap (from what journalists have said) and requires a lot of planning (I believe Shawn Layden said they start planning for E3 sometime around January). Sony probably determined that the costs outweighed the benefits this year and decided it was better to not go. Days Gone should be out before E3 2019, which would only leave The Last of Us Part II, Death Stranding, and Ghost of Tsushima. We've seen a decent amount of footage from each of those games and all that's left is to announce release dates. With God of War, Spider-Man, and Days Gone having their release dates announced on the Playstation Blog, they'll probably do the same for the remaining three exclusives.
I expect they'll be back at E3 in 2020 once the PS5 has been officially revealed at PSX 2019.