Yes. The assemblies created by the Assembly Plugin is attached to your project so it gets deployed too.
Yes. You can refer to it using the id of the assembly as the dependency classifier.
The Javadoc Plugin can generate the javadoc files of your projects. Also, the Javadoc Plugin can package them!
Please see the Javadoc Plugin Documentation.
The best way to handle a mixed bag of dependencies with and without classifiers is to use the ${dashClassifier?} expression, added in version 2.2-beta-2 of the assembly plugin especially for this purpose. This expression will determine whether each artifact has a classifier, and if it does, it will substitute the artifact's classifier - prepended by a dash - in place of the expression.
For example, suppose you want to include two artifacts, commons-logging-1.0.4.jar, and yourserver-1.0-client.jar (where 'client' is the classifier of the second artifact). To do this, simply add the following to your dependencySet:
<outputFileNameMapping>${artifact.artifactId}-${artifact.version}${dashClassifier?}.${artifact.extension}</outputFileNameMapping>