Half cover is not ignored:
Cover rules say:
A target can benefit from cover only when an attack or other effect originates on the opposite side of the cover.
Specifically for half-cover (emphasis mine):
A target with half cover has a +2 bonus to AC and Dexterity saving throws. A target has half cover if an obstacle blocks at least half of its body. The obstacle might be a low wall, a large piece of furniture, a narrow tree trunk, or a creature, whether that creature is an enemy or a friend.
The reach property of a weapon states:
Reach. This weapon adds 5 feet to your reach when you attack with it, as well as when determining your reach for opportunity attacks with it.
Putting all this together (assuming every creature takes up a 5 foot space):
With a reach weapon you can target the enemy creature, even though there is an ally between you two. However, the attack is still originating from you. With that in mind, the target gains the benefits of half cover, since a creature is standing between you and the target, and the attack is originating from the other side of cover. There is no specific rule (for example, like the sharpshooter feat) that allows your attack to ignore half cover in this case, so the target keeps the benefit of half cover.