There are already individual aircraft numbers in IL2, but the rest of the skin in the stock campaigns is usually "cloned" for aircraft of the same squadron. Think of it as the skin being the base for all of the squad's aircraft, with individual stencils applied for the aircraft codes.
As for other insignia, a lot of squads have their own and in many cases these are already represented in IL2. So, thus far i really have no doubt that what you're asking about is going to be included in the new sim as well since it was in the old one to begin with. However, what will really set individual planes apart in the new sim will be the application of weathering on a separate layer.
I guess the base camo/skin will still be the same and each plane will have its own code, but with weathering applied the new planes will look factory fresh while the old ones look worn out, with flaked paint and long exhaust and gun port streaks. In IL2 you have to manually change a skin yourself to include such things, but in the next series of sims the aircraft will age on its own as you fly missions.
For the axis insignia now, the fact that Germany outlaws the use of the swastika means that probably any european distribution of the title will not depict it. As explained before, this is done so that the game can be sold in Germany but there will probably be modifications or custom textures added later on by the users, just like it happened with IL2. As for luftwaffe squadron insignia, there's a guy from the community here in these forums that has taken it upon himself to research each and every one of them in order to ensure maximum historical accuracy.
The short answer about the things you ask for is, we'll get some of it because it was already in IL2 and not having it in SoW would be a step backwards, we'll get some new things too from Oleg's team and their new technologies, community members are providing extra feedback and material to fill in the blanks and whatever you don't get on release someone from the community will probably provide later on. So, sooner or later you'll probably get everything you ask for markings-wise
