Well, enemy fighters do have flares and they do not hesitate to use them -- it's that theirs simply don't work. Right now the game is not very well balanced and needs lots of polishing in the future.
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About the indication of missiles, there are 4 numbers on the right down side of the HUD, I still can't figure what's 1 meant for, but 2 shows how many missiles current ready for fire, and 3 shows how many missiles are in reserve. 4 shows the currently selected missile type.