HoMM3 HD is a mod (add-on) for the game Heroes of Might and Magic 3.

1) This is a question for the te-wt script writers (I am not one of them). Although I even know where to look: script02.erm. The script is based on the fact that there are 5 clickable hero portraits with numbers 39 - 43 and 5 clickable city icons with numbers 32 - 36 in the game.
But in HD, there are 8 hero portraits with numbers 39 - 46 and 7 city icons with numbers 23 - 29. This makes it clear why ctrl-click only works on the first five heroes and doesn't work on any of the cities.

2) It is possible. HiRezData\HiRez.ini parameter #8