Sometimes parenthesis means it is a "ghost" note. It is a note that is played, but barely recognizable. You sort of hear it being played, but its not accented very strongly. For example: Pick a string on your guitar at a normal force, then pick one very lightly. The one you picked lightly is very faint. If you played both at the same time, the faint one could be a ghost note, since it isn't really heard a whole lot over the one you picked harder.

This is what I have always though at least. I could be wrong.