IIRC, mass relays were a bridge to instantly move to other space systems, they seemed to create a black hole (that Joker was trying to get away from) but he seems to have landed in another land. I'm guessing that nobody really died, but they're now stuck in whatever system they were while the mass relays exploded, a user in NeoGAF posted that there's a Codex entry that says that ships can actually travel light years in matter of days. So if the planets are somewhat close, they can get back to them with week-long journeys, but the problem comes with the far away planets, those might take a longer trip to get back. Maybe they would end as the Migrant Fleet of the Quarians, or find a new planet to establish. If Joker survived, I'm pretty sure some ships escaped the explosions of the mass relays, that's my take on it.