How do views Contextual Filters behave with Pathauto? I have Pathauto installed, so URLs to nodes are not like node/3. My question is that if I write a View with a contextual filter for looking for node/3, will it work?

Note: This contextual filter is in a block. See this question.
You would get the node id(nid) as argument. Internally the system gets its data from the unaliased url, not the browser url created with path_auto.