The first point that I personally believe makes the Iron Knuckles (in LoZ anyway, never played the other classic Zeldas) an extremely tough enemy to face, especially when compared to that of the Iron Knuckle in OoT and MM or the Dark Nut in TP, is that you can only attack them from one of four directions, you don't have the ability to face in any direction in a 360 degree manner. This reduces the oppertunities for which you can hit the Iron Knuckle to much lower than that of the Iron Knuckle's in the newer games.
The second point that I believe contributes to the toughness of the Iron Knuckle's in LoZ is that they do not have an easily predicted path, infact, as far as I'm aware any for of prediction on which direction they turn and when is just pure luck. This makes it harder to attack the Iron Knuckle's as they can turn in your direction at any second to land a massive blow to you to greatly reduce your health. This combined with the fact that you can only turn and attack an Iron Knuckle from 3 directions along with their lack of ability to turn in any more than 4 directions, greatly increases the chances that the Iron Knuckle will turn towards you to land that blow.
The third and final point which I believe makes the Iron Knuckle one of the hardest enemies to beat in the entire game is that unlike newer games, they aren't exactly slow and thus move quickly (once again, unlike newer games). This further combined with the fact that the Iron Knuckle isn't predictable and that both Link and the Iron Knuckle can only turn in 3 directions makes the challenge of hitting the Iron Knuckle a rather tough one. You need to get close to hit but when you do there is always the chance that the Iron Knuckle will turn very swiftly and hit you hard, making your job much tougher.
As i've explained above, these 3 reasons are what I believe makes the Iron Knuckle such a tough enemy on LoZ, and this toughness is sadly what the newer Zelda games are desperately in need of.