Dependency injection (ninject) using strings, anti-pattern?

Is this code smell ?

Yes. Either create a ConfigurationRepository or create a factory/builder (two different design patterns) which creates the different services and then register that factory/builder in the container instead.

I got an issue with this code too:

kernel.Bind<IUser>().To<User>()
      .WithConstructorArgument(@"username", configuration.Username)
      .WithConstructorArgument(@"password", configuration.Password);

A IoC container is primarly not used to create domain entities but to create services/repositories/controllers etc. i.e. to create the objects which control the flow in your application.

I would prefer to use ToMethod() here:

kernel.Bind<IUser>()
      .ToMethod(ctx => new User(configuration.Username, configuration.Password));

If the User constructor has other dependencies, then I would defer to @jgauffin's answer.

You could still use ToMethod() with Kernel:

kernel.Bind<IUser>()
      .ToMethod(ctx => new User(configuration.Username,
                                configuration.Password,
                                ctx.Kernel.Get<Foo>()));