Back then, most NBA bigs didn't take a lot of three-pointers, so it's by design. It was accurate then, not so much now.
There is a field in the players.dbf file called
THREEPTATT, which determines the percentage of a player's attempts that will come from three-point range. Changing that value (it's a percentage out of 100) will, in theory, allow a player to shoot more or fewer three-pointers when controlled by the CPU.
More information on the players.dbf file can be found
here. The easiest way of changing that value is to open a saved roster with
DB Commander, find the player you want to change, scroll across to the
THREEPTATT, and enter a new value. Move to another cell (box) in the database to save the change automatically, close DB Commander, and load the roster in-game.
I can't guarantee the results will be perfect or even satisfactory, because a game like NBA Live 06 does have AI that's certainly outdated by current standards, and again, it was designed to mimic the style of play in the NBA as it was 12-13 years ago. But that's the attribute to experiment with.