The way I'd answer this is that it's less important for what matters (comparing players to one another) whether the height is accurate absolutely as translated to the basketball court; instead it's more important to understand how players height relates to one another.
If you could guarantee that someone's height measured in shoes never changes throughout their career (that they never use different types of shoes than the ones they measure with at the combine, for example), then you could just as well use the height in shoes as a good way to properly compare one player's height to another. Otherwise, we're stuck with shoes-off height as the best way to make the player-to-player comparison.
EDIT: As long as some players seemingly add 2.25" to their barefoot height with shoes, while others add as little as .75", the height in shoes measurement is just too misleading to help us usefully compare one player to another (again assuming that players will sometimes change shoes, which I don't know why I shouldn't assume).
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