As for Kaito's death, I didn't really feel sad at all because of how I don't care about him. I will give the episode credit in that they handled his death pretty effectively, more so than most of the other deaths in this arc for that matter. They actually gave his death individual attention, instead of cramming in a bunch of deaths in one episode like they have for everyone else that wasn't IV or Durbe, and there were some nice lines and moments with Kaito and some of the other characters while he was dying. Although, Dr. Faker and Haruto crying out to him felt too emotionally manipulative to be effective. Dr. Faker hasn't appeared since the end of the first season, Haruto appeared a grand total of two times before this duel, Haruto has no personality and Kaito has barely interacted with either of them. Their appearances just felt like an attempt to make the audience feel sadder more than anything meaningful within the context of the show. If there had been more of a family group dynamic between all three of them throughout this second season, as well as give Haruto a personality, then their sadness could have had more of an impact on the audience.
That has been one of my main issues with the deaths in this arc. Most of them feel too emotionally manipulative in a way. It's like the writers want people to feel sad because of the number of characters that have died, rather than simply the fact that they've died, considering how quickly they've killed most of them off. The deaths in GX's third season had more emotional impact because most of them were killed off individually and the ones that were killed off as a group was done so to further drive more psychological trauma for Judai in order for him to become the Supreme King. Although, they also had generally better characterizations and more fleshed out personalities than most of the Zexal's cast for me, so that plays a part of it too. To be fair, they are in the last arc too, so they can't spend as much time as they probably could have if they had a bit more time, but it's still problematic and prevents the deaths from being as meaningful as they could be.
Even so, they handled Kaito's death pretty well and I was surprised with how dark it was. He wasn't turned into Barian energy dust like everyone else, but he dies on the moon, or dying assuming the air in the suit didn't go out the moment the system wasn't operating. I still couldn't really tell why he cared about being a Dragon Tamer though. That was one of the reason this was the weakest subplot in the season.