As far as I can see, in Konsole both CTRL+ENTER and ENTER look like byte 13 in the stdin of the running app. But when I run mc which obviously uses ncurses lib, pressing CTRL+ENTER inserts the name of the file into the command line while ENTER opens the file. How is it implemented? I tried to look into sources, but they are totally unreadable for me.
mc (midnight commander) doesn't use ncurses for input, but may use it for output. Essentially it is looking for specific character sequences.
mc makes little use of the terminfo database, essentially only to check on the xterm mouse- and alternate-screen features.
In principle, it could read the user-defined capabilities from the ncurses terminfo database (see for example ncurses trapping extended keys (Control-left, Shift-Function etc)), but it does not.
Since you are looking at sources, see the source of mc, in lib/tty/key.c, which contains tables which mc uses as a set of predefined keys. Doing it that way "works" when mc is configured to use slang, for instance, though it has the drawback that it's hardcoded and may not actually match your terminal.
However - as I said, mc does its own input. Further down in key.c, you may see a chunk in get_modifier() ifdef'd with HAVE_TEXTMODE_X11_SUPPORT. Inside that is a call which ultimately goes to XQueryPointer, which mc uses to find the current state of the modifier keys — if it happens to be running in an X display, and if the feature is enabled. You are probably seeing that.