Does the need to actively identify a creature type go away if we instead think of favored enemy bonuses as due to something a Ranger's always doing? In other words, his fighting style is most heavily influenced by his favored enemies (bonus), but he doesn't specifically change tactics for them. Rather, he's developed a fighting style that's generally effective, but which he's discovered is especially effective against the opponents he's focused his hunting skills on?
That sort of thinking might carry over decently to the skill bonuses, too. He's not actively applying "I know elves think this way," to a Sense Motive roll, but the body language indicators he depends on happen to be those most prominent in elves.
This is the key - if we assume the Ranger adopts an especially bizarre fighting style only against his favoured enemy, then he needs to know who they are to combat them effectively. But, if we take the extreme "their heart is in their leg" example, wouldn't using that style against a human make the Ranger
less effective, rather than just normally effective?
The RAW says he gets "+2 bonus on weapon attack and damage rolls against such creatures.", not that he gets his bonuses if he knows he is dealing with such creatures. This seems to indicate his fighting style is no less effective than normal against other opponents, but is especially effective against his favored enemy.
The skill roll bonus is similar. It seems unlikely the ranger would typically KNOW he is making a Perception check to spot an ambush laid by Elves, rather than one laid by Gnomes, or wolves, yet he should get that bonus to his Perception skill. If he is looking for tracks, he won't know there is a Magical Beast in the group he is tracking, but he should still get the bonus to his Survival roll. He might be using his Perception to penetrate the fact his Half Orc enemy is disguised as a human. Assume his PER bonus, without FE, is +8, and the DC is 20. If he rolls an 11, does he fail (no FE bonus because he doesn't know the disguised person is a FE), or succeed (he gets the bonus because he is using the skill against his FE)?
Given the volume of "what if's" and corner cases if we assume the Ranger must know the target is a FE, it seems like the best approach, even if the rules were less clear, would be to apply the bonuses whenever the FE is the target.