I know it's by player choice of course, but it's the ATP's computer, other sports when players retire remove said player from their stats etc. so why not tennis, and you can't expect the ATP to wonder if that player will come back, which they usually probably won't, they can't be dealing with that, as I said before it's not fair to active players to have retired guys taking up their spots, like for instance when Roddick made a big deal of his retirement, I think it's quite certain he won't be coming back, so there is no point in having him still in the ranking.
When is a retired player removed from the computer btw, when the season ends?
In Formula 1 (which really sucks, but is a good example), once a pilot retires from the race, he is not immediately thrown into last place, unless all other remaining drivers pass him. Thus, Andy Roddick has won points and it would be "helping the other tennis players" to simply have them all advance one place for free. Throwing Roddick's points away (which he earned) is not really fair to the sport. If other players want to be ahead of him, they must earn the points he earned.
Any retired player that does not specify he wants out of the rankings is taken out once all his points are dropped. Out of the computer, never. Any player that has played at least one tournament on ATP or Challenger level or gained one ATP point is in the computer forever.