It's doubtful the US ladies or Pairs will (not just because they have no chance at the individual event, but also because the US Team has absolutely no one else to send in the Team Event if they want a legitimate shot at the medal). But it will definitely work out with the Russian ladies - they can have 5 olympic medalists from a single Olympics. It will also work out for their Pairs - they can send Tarasova/Morozov, Panfilova/Rylov, Boikova/Kozlovskii to the Individual Event, but Mishina/Galliamov or Pavliuchenko/Khodykin along with Panfilova/Rylov in the Team Event. They will not dig deeper in their men's field of ID field because the ones they send to the Individual Event will already be the ones who will get them the necessary points in the Team Event.Thus, if they could only pick one, they would much rather skate the team event than the individual event. However, since they would presumably be the No. 1/2 US Pair/lady, they would probably just choose to skate both to have the best of both worlds.
I think it will add a layer of strategy. Plus, since the Team Event is supposed to be about deepening and broadening your fields, why not?
In the Japan situation you explained, it could work if they really wanted to have two ice dance teams, but I feel like it's far more likely for them to want to split their singles disciplines so that their top skaters can conserve energy for the individual event, since their top skaters in the singles disciplines have a chance at an individual medal. Also, the team medal is a better reward for their singles disciplines, which are far stronger than their paired ones.
Again, it's a matter of strategy. They might not want to use any substitutes at all if they so choose. But they can send Hanyu for both men's events and Kihira for both ladies events. And then they can send two Pairs and two ID couples just for the experience since they're probably going to lose in those disciplines anyway. OR as dancelion explained, they might want to preserve their top singles skaters for the individual event - so they'll play their extra skaters there so that can get the Olympics experience.I don't think any top skater will refuse a potential medal to someone 3rd-4th in the row.
Another layer of strategy: Are Sinitsyina/Katsalyopov going to the Team Event at all, or will they gamble it all on the Individual Event and end up with zero Olympic golds? What about Sui/Han? Is Alexandra Trusova going to do 4 quad programs at the Team Event and then bomb the Individual Event? This applies to many top contenders of many national teams.
ETA: Not sure if that made sense or if it's at all a good idea