Why Drupal adds <br /> tags to markup entered in "Full HTML" view?

It's there to help the majority of people who want to enter a newline in the textarea and get a newline. Without it, everyone everywhere would be getting all their text in one solid block. impossible to read.
People don't like that. Nor should they need to enter p tags by hand either (unless, like you, they choose to). It's a feature.

Well, as you can see, it does act correctly as a break versus as paragraph (single line break inserts <br /> and adding an additional line makes it behave as a paragraph). This is how Drupal has worked for many years, and I doubt this aspect will change (many people really like it, including myself). For average daily writing in Drupal I (and many others) find this much more preferable over writing those extra tags. I simply keep in mind that they will be inserted when the page is rendered, and this keeps my content editing process cleaner and simpler. I also keep most of my more "intricate" HTML in my template files, and tend to only use basic formatting in the content itself, and sometimes lists, links, etc. I like to use BUEditor to simplify this on my own site (it is an HTML tag inserting editor, not wysiwyg, which you can customize to add any kind of tags you want). Other people choose to use a full wysiwyg editor, and with those the documentation often advises you to disable the Line break filter, as the editor may insert those tags automatically as well. The "average" Drupal user actually wants an optional "full wysiwyg editor" in core, not more HTML to write ;)

Though the presence of the Line break filter won't likely change, what can change in Drupal is the help text or other indications of what is happening. For that, if you have specific ideas on the issue and how to make it better, you should submit them to the Drupal 7 issue queue (it is not too late for suggestions to make it into the next version). For instance, perhaps you might suggest that if the administrator is logged in (not regular users since you wouldn't want to show them such things), some extra help text is shown in the input formats help text, directing them to where they can configure the input formats (and best practices for doing so). It will help most if you give some concrete ideas about what you think it ought to say that would have made it clear to you.

In Drupal, the best practice is to use Filtered HTML for all users other than yourself or other high privileged users ("not" visitors or regular users). Full HTML can easily be abused to break (or even hack) your site (given access to every possible tag, there are a variety which a malicious user can use for unfriendly purposes). You should simply add any HTML tags you do need generally available to the filtered HTML list (of course only allowing those you are sure will be safe), or you can make your own Input Formats as well if you'd like. Personally I do not even give Full HTML to the user accounts I set up for clients to use on their own sites (unless they specifically want it) as I try to protect them from breaking their own site... often the first thing they do otherwise is paste in some craaaazy code that borks the whole page, or perhaps directly embed flash or videos instead of using the specific fields I made for them to do those tasks with.

Hope this helps.