I worked at a newspaper for 5 years, and their editorial system - this would be the software that reporters write their stories in, editors edit the stories in and proof readers and copy editors lay out pages in, not to mention ad placement, classified pagination and much more - was pushing 10 years old when I started. It wasn't integrated with the website content management system. It was slow, outdated and very annoying.
But it worked, everyone new how to use it, and we knew that we would be able to publish multiple publications every day, 365 days a year. The fact that the system wasn't fully integrated with the CMS meant it was difficult to add links to stories, usually requiring going into the CMS and hand-coding links, after waiting for the publishing scripts to grab the story and post it, a process which could take up to 30 minutes, depending. Typically an online editor or copy editor, far removed from the research and work the reporter had done, would manage this for the entire website, since it makes more sense for the reporter to be out on the street doing actual reporting.
So the 'simple' task of adding a link isn't as simple as it seems when placed in the context of a fast moving newsroom. Typically the battle isn't "why isn't there a link to that source document?" but rather "what do you mean you can't get anybody to speak on the record" or "we need a story for the 1A centerpiece now."
And then the next day the same battles start all over again, the process repeats and another newspaper is printed. It's difficult to change the process because the process is so critical to meeting print deadlines to be able to deliver papers on time.
To add to this, newsrooms are getting cut down at the same time they have to do more. My newsroom once had ~60 people at a time when all they did was print the paper. When I left, it was about half that size and we were posting regular online updates, tweeting, linking to stories from facebook, monitoring comments online, posting photo galleries, shooting video and creating interactive flash presentations on top of it all.
So, yea, if the reporter has time, he reads the report. If it's a story about calf length, it's more likely he'll skim it to be able to bang out a space-filling (or traffic driving) story. And since it's a light human interest story, and not something that's likely to get the paper sued, it gets a quick once-over proofread, then posted to the internet ASAP, then printed, and everyone is on to the next big story to feed daily monster that is daily publishing.
I still think some of these organizations will get there. The New York Times is leading the pack, but the slower publishers will take awhile to replace their antiquated systems and change the daily process that has been refined and perfected since the dawn of the printing press. Of the ones that don't, new organizations that can manage the digital realm will replace them.