Where is the list of sidebar's favourites stored in macOS Sierra?
Thanks to @TonyWilliams for the starting point and after a brief research I realized that requested sidebar's favourites are stored actually in directory ~/Library/Application Support/com.apple.sharedfilelist/, the file com.apple.LSSharedFileList.FavoriteItems.sfl among other files which are responsible for other sidebar sections. But those files are not available for easy editing.

Starting from OSX El Capitan and newer versions there is a command-line tool sfltool availabe to make some operations with that files, such as add an item.
But this tools doesn't have ability to remove items (the root of my problem which causes to this research) and I found another good tool on GitHub called mysides
which allows to remove items as well.