1- After the reboot everything that is in the sandbox will be automatically terminated and won´t be able to execute (only after manually execution).
No it will run in the sandbox again after the reboot, unless removed from the sandbox in some way, for example by the user making it a trusted file. Because it is sandboxed it is unable to damage your system.
2- If my first post is right, then that means after the reboot you will not receive pop up´s from those programs (like com windows hooks, COM interfaces, etc).
You will receive the same pop-ups, if the app is still sandboxed. Most sandboxed files don't generate COM, hook alerts, but some do.
3- Can an other program (trusted or not) start an application that was terminated in reboot (and of course is in untrusted files).
If an unknown program is started again it is sandboxed and so unable to damage your system.
4- Manually terminate an application that is in the sandbox will have the same effect than rebooting ( the application won´t be able to automatically start).
If an unknown program is started again, whether automatically or not, it is sandboxed and so unable to damage your system.
5- what about dropped files
Sandboxed software is not allowed to drop files in protected directories.
Hope this answers your questions. Apologies for the delay.