Suppose there is a website at example.org, as proven by google results. Now there is also a domain example.com. It aliases to example.org. Google doesn't find any directories on that domain. How can I now for sure if example.com (or its subdomains) are used to serve (unspidered)pages or mail? Or can I be 100% sure that it's only use is an alias, just because searchengines don't see it?
Not entirely sure this is what you are after but you could do a reverse DNS lookup on example.com and see what sub domains are set-up you could then query those domains or attempt to visit them in a web browser to see what content or services they are serving. I use this site for Dns lookups : http://network-tools.com/
As @Rao says if you rewrite all the requests from B to A that is all Google will see.
For what i understood from you question i have this to share. If you activate the domain alias, but create a .htaccess rewrite to send all domain "B" requests to domain "A", Google should only see a single site.
I personally used it.
correct me if i misunderstood it.