My own headcanon is that, while they do eventually reconcile and become friends after Eclipse Lake, it may have taken them slightly longer to do so compared to the rest of the Hexsquad. I think that it could interesting for them to initially be somewhat awkward and avoidant of each other, not out of hatred, but because they could be unnerved by how much of themselves they see in each other (in addition to feeling guilty about Eclipse Lake for their own reasons). However, at some point during the time-skip in TTT (or even during the one in W&D), the two could eventually find a moment to put their past behind them and become friends.
As for their dynamic following this, I think that they would definitely bond over sharing abusive upbringings, but I think that it could also be fun for them to be competitive in a friendly manner. Additionally, I think that it could be really funny if, whenever they work together, they have an equal chance of either being a highly effective team or literally having one brain cell shared between them with no in-between whatsoever.
But that’s just my brief headcanon on Amity and Hunter’s dynamic. Which do you have?