After looking through the WFRP 4E core rulebook I cannot find any information on the difference between the melee specializations polearm and two handed and all the weapons listed under the polearm category are 2h weapons. My question then would be is there any difference? And if not why would anyone choose the polearm specialization?
You might be confused by the difference between "Two-handed weapon" (written TWO-HANDED) and "weapon that needs two hands" (written (2H)). They are not interchangeable and mean two different things.
The two handed weapon skill works with the weapons that are listed under that weapon group (the table headlines) in the weapons table. The polearm skill works with weapons under the polearm group. Basically, there is one skill per group that works with exactly those weapons. So you cannot use the two handed skill for a polearm, because the polearm is not in the two handed weapons group.
The little (2H) markings have nothing to do with skills and only mark how many hands you need to use that weapon, so you know whether you can wield a shield or second weapon or other items at the same time. No matter how many hands you need, you still use the skill that that weapon belongs to.
So for example: Spear, zweihänder, shortbow and handgun all need two hands to operate as symbolized by the (2H) in front of their name, but they all use the skill of their respective group: Spear uses "polearm", Zweihänder uses "two-handed", shortbow uses "bow" and handgun uses "blackpowder".
As to why would one use a polearm over a two-handed weapon: polearms are the weapons of peasants. Widely available and cheap. Two-handed weapons are the weapons of richer people, mercenaries, nobility, clergy or guards equipped by rich merchants. Costly and often scarce. For comparison, you could buy 66 spears for the price of a single zweihänder, even if both were readily available. Warhammer is not really the system where you play rich people. It tends to be dark and grim and not as shiny as other systems. So polearms might not be a good choice from a purely system min/max perspective, but they might be what your character can realistically get. A spear in your hand might be worth more than a zweihänder in your dreams.
Two-Handed as a skill specialization is for weapons in the "Two-Handed" category: Bastard Sword, Great Axe, Pick, Warhammer and Zweihander. Weapons in the "Polearm" group are covered by Meelee (Polearm), in the same way as the two handed Military Flail is covered by Meelee (Flail). So there is a difference between the two.
Now for the "why" of polearms: @nvoigt gave a great answer on the issue of price and availability, so I won't go into a lot of details for that. Polearms on average are cheaper (especially given the rules on keeping money between adventures), less conspicuous, and more available.
However they do have one, fairly significant benefit in a mechanical perspective as well, and that is "Impact". Most polearms have the Impact quality, and while they might cause less direct Wounds damage, they have a significantly greater (double if I see correctly) chance of scoring critical hits. Against enemies with lots of Wounds and high Toughness/Armor, critical hits can be a much more effective way of finishing the fight compared to trying to whittle down the Wounds of your enemy to 0. Combine it with the longer reach of most polearms and you get a weapon that is more effective against the more monstrous enemies one can run into during their adventuring careers.