I'm expecting the main show's to be merged onto one Earth, but for new shows and new Earth's to still be found and explored in a still-existing multiverse.
I still don't think there's any point to merging the universes, and a lot would be lost. Why would Supergirl set up this season-long villain arc with Leviathan as these ancient beings "defending" the Earth if they were going to permanently destroy the Earth that Leviathan was associated with? Why send Malefic off to fight for peace on Mars, then destroy Mars a week later?
The fundamental difference between this and the comics is that the comics rebooted their whole continuity from scratch, reinvented the characters and their backstories as a single universe. That wouldn't work here. They're not going to reboot the characters. The individual shows still have their own distinct story and character arcs in progress. Merging their universes midway through the season just doesn't fit into that. As a season finale, hypothetically, maybe. It's not unprecedented for a show to do a wholesale continuity reboot between seasons, like when TNT's Witchblade ended season 1 with a time loop that reset everything to the beginning. But midseason, with ongoing seasonal arcs still in progress? I just don't see that working structurally.