The only way I can see 3D consistently work for games like Trauma Center and Contra games is that the 3D effect is able to come out of the top screen but towards your point of view at the bottom screen. This means the player is able to do the surgery in the bottom screen with the 3D effect covering the bottom screen as a layer. When the player looks back at the top screen, the 3DS camera will sense the player's shift of vision, and the 3D effect will now be at the top screen. Basically the 3D effect from the top screen can reach the player's vision of sight at the bottom screen and appear normally.
For games like Contra 4, this could be hectic since players find it easier to look at both screens at one time, so it might force the player to only look at one screen at a time but have the 3D effect carry over to the bottom screen. Think, for example, an enemy in the top screen shooting bullets and when you look back at the bottom screen, you now get the 3D effect of enemies shooting at the bottom screen, but the bullet from the top screen will be visibly ontop somewhere by depth of the 3D effect.
I'm not sure if that made sense, but I hope it helps brainstorms possible ideas of how 3D can work games like Trauma Center or Contra.
