Where it is referred to as the "Ricky rule" (as in running back Ricky Williams)
https://www.racked.com/2018/2/1/16955990/nfl-long-hair-ricky-rule
It appears that prior to 2003 the rulebook was merely silent on the matter. That, of course, leads to ambiguity and divergent calls by different officials. Hence the need for an explicit rule. Confusion in 2006 would be understandable for a relatively obscure and rarely invoked rule.
There are other articles I have seen commenting on other rule changes since then which further emphasize in various ways that the hair is considered a body part. For instance, various rules which have to do with whether or not player A touched something (the ball, or player B) have been amended to include the hair in the list of body parts which count as having touched the thing in question.