Many companies use Customer Relationship Management (CRM) systems to manage interactions with their customers and potential customers.
There are many CRM systems, but most are proprietary, expensive, and, most importantly, none are designed to work with print publications.
Typically, print publications will cobble together their web operations using different systems that don't talk to each other.
They may use Mail Chimp or Constant Contact to send out newsletters, but that mail list can't interact with a list of donors on Network for Good or PayPal. Similarly, commenting is done on a third party system such as Disqus or LiveFyre.
We don't know! Subscriber databases are usually kept at a fulfillment service that's distant from the home office. And subscriber mailing lists rarely include email addresses.
Most publishers have no idea who their subscribers actually are, and have no way to communicate other than to mail them an invoice or renewal promotion.