In WAP model, you don't have any issue in any level of directory depth inside it. In C# it will be dot notation to access usually. Except you create your own namespace and class naming guidelines.
If in your App_Code directory structure is like below :
App_Code
--> BusinessLogic
--> Common
--> Report
--> etc
--> Shared
Then, for example, in WAP model you can have a module structure like this :
MyModule
--> images
--> js
--> BusinessLogic
--> Common
--> Report
--> etc
--> Shared
--> BusinessInfo
--> UserControls
--> etc
That's not a problem. Just put your code inside your App_Code and also it's folder inside your WAP module project.
CMIIW.
HTH.