Is there any tool in some PDF Viewer/Editor like Acrobat, Evince, etc. where I can navigate and watch coordinates(i.e. (x,y)) of any selected point in PDF-document?
CanOpener is a very impressive tool for working with PDF files. It operates as a plugin for Acrobat Pro - http://www.windjack.com/product/pdfcanopener/
Another option would be to use the Foxit Phantom PDF Advanced Editor which allows you to select objects and see the properties of each object.
You could use a library such as Quick PDF Library to render the image to a BMP file and then write yourself a little TOOL to scroll and zoom around the BMP file reporting back coordinated. http://www.quickpdflibrary.com - (Note : I do consulting work for Quick PDF)
I am sure you could load the PDF into Adobe Illustrator and get the current coordinates in the status bar.
Andrew