The short answer is YES.
"Is it possible to use Ninject in non-executable dlls, which do not have a main method, and how?"
Dependency Injection is made to separate implementations from each other.
Your DLL plugins can have interfaces (expect interfaces) without any tangible classes.
but all these dlls will eventually run in one EXE, and only in that exe you will have the registration of (interface, implementation) .. where your dll will resolve whatever it needs.
Now, sometimes, you want to have the registrations in your DLL themselves ... In which case you need to expose that method to register and call it from outside i.e. from the EXE .
I hope I answered your question in a way that is clear.