I shouldn't really need to explain this, it is written there on the site in black and white:
"The RDS can be used by law enforcement, government, and industry organizations to review files on a computer by matching file profiles in the RDS."
Sorry, I'm still not sure how NSA is involved in this project. Much like any open information, yes, it can be used by industry organizations, law enforcement and government.
The information the list contains is not personal, it's not secret, and collecting it is a trivial job. The potential use of it to infringe upon personal rights is similar to that of a shoe -- a pretty useful tool for all sorts of things, but sure, you could figure out a way to hurt someone with it.
"This will help alleviate much of the effort involved in determining which files are important"
Clearly it is intended for mass remote surveillance, they're not even bothering to hide the fact. Once upon a time (pre-Snowden) that viewpoint might have been considered paranoid...but not anymore...
You're making quite a leap there. This information is about as useful in mass surveillance as super soakers are in fighting wildfires. The NSA likely use more sophisticated file signatures than a bunch of rigid checksums in a list that is updated less than once a month. More importantly, they probably focus more on what is being communicated over networks than what legitimate software is installed on a person's computer. The part that you quoted but cut off before it contradicted your conclusion puts the likely use of this in law enforcement quite well: "This will help alleviate much of the effort involved in determining which files are important as evidence on computers or file systems that have been seized as part of criminal investigations." A seized computer is often scanned for documents, and identifying the software installed can greatly narrow the search for those without the budget for more sophisticated means.
The way software update cycles are nowadays, the worst I can see in this list is a waste of money and effort.