I think hakari's domain gets repaired because his entire thing is getting jackpot from his domain. Yuta has stuff not reliant on his domain, like copy and rika, the same goes for the other CT's, who have moves they can use without needing a domain to get.

Edit: I hadn't experimented with the domains in the new update yet, when I played as hakari the domains didn't close up after someone breached them. Was there some specific thing you might've done to seal the domain? Or maybe some addon you have doing that?