If there is unread notification under the bell icon I would expect that after clicking the notification link it turns automatically as read (instead of manually clicking read checkbox) Is it possible to configure it that way?(or if you can direct me to the file/piece of code that I can change?).
Opening the notification tray doesn’t mean you’ve read them all. It could mean you wanted to read a few and the others for reading later. Also, imagine there are 100, you can’t see them all at once. If you wish to discard them all (i.e. mark them all as read you have the “clear all” button that you can use.
I don’t think it is.
Sorry I didnt make myself clear. I meant when I click specific link (URL of one notification item) - see the picture - i would assume that this item is implicitly read and system would change status to read (so i dont have to click on the read checkbox of this item manually)
ok that makes more sense 
I agree that it could be nice to have that. When do you consider it’s been read?
- when the link to the page is clicked?
- when the “…” is clicked and one of the diff links clicked?
- when the “author” link is clicked (probably not)?
Feel free to open a jira issue at http://jira.xwiki.org/projects/XWIKI/summary with a clear explanation of how you’d see it working.