I believe in this case that the Hunters would have 0 threat throughout the phase regardless of their Clue boost, this is because Ithilien Tracker does not say "printed threat" and just "threat".
What's interesting is that it creates an anti-synergy with cards like Spirit Merry. This is the main difference tactically between it saying "does not contribute threat" and "reduces threat to 0". Cards that trigger of off threat (and not printed threat) will be turned off for that one phase (almost always the Quest phase).
Wait, Spirit Merry's effect triggers on reveal and Ithilien Trackers ability on entering the staging area. So you could still use Merry's effect and then reduce the enemys threat to 0. That should work.
Ok, now to clarify: We don't have a difinitive ruling on "until the end of the phase" effects on player cards. Alright, I just play it this way:
When Hunters from Mordor enters the staging area he gets 0 threat regardless of his Clue bonus, but if another Clue card is revealed after him (during the same Quest phase), he gets a +2 Attack and Threat strength boost.