I Can See Clearly Now

Many scientific studies are done daily. The studies that are actually published, to my surprise, are often tweaked to "appeal" to the readers.
An interesting article I found that explains this Transparent Science talks about how much these studies actually disclose their information.
"In an ideal world, science is objective: the results of an experiment should be evaluated without massaging the data or manipulating them in any way."
I use to believe that whatever a scientific journal/article published was 100% open. As I read more about transparent science, I became aware that most studies published are what the public wants to hear/know. Either that or the study tries to shock the public and often only discloses the things that would get their point across to their audience.  
It's really interesting to learn how much the world has changed. While there is so much more information out in the open, the legitimate resources available  might not be able to be trusted to be totally disclosed.
In the article, it states that in 1997, only 1% of scientific journals actually had a disclosure statement. 
Makes me wonder how clear everything actually is. Is anything transparent these days or is it all behind a blurry window?