You are right, but adding something from IV to III's map which is existing in both IV's and III's Liberty City won't ruin Rockstar's Vision like Times Square, it is existing in both maps but it's more detailed in IV.
Liberty City (atleast, GTA3/LCS' rendition) isn't New York, it's a mix of several places (Chicago, Detroit etc). Adding the SoH or Rotterdam Tower would simply ruin Rockstar's Vision™
I don't think Times Square in III was trying to be too accurate to real life Times Square. And even then, there's other cities all over the world with Time Square-esque neighborhoods.