With respect to Junkers, I personally could see them being possibly an ally to HF. The reason for this would be because of the way Liberty have recently treating them. I am sure they would probably like to secretly get back at Liberty by supplying a thorn in Liberty's side. Junkers are basically your neighbours. They also have access to a multitude of resources.
Having Trade Agreements with Groups who are enemies to each other is widely accepted within the Game.
Liberty is at war with Rheinland but Bretonia, an ally of Liberty, still trades with Rheinland. It seems as though Trade Agreements, within this Game, is a way to circumnavigate certain Alliances. Even before Gallia attacked Bretonia, Bretonia was still Trading with Rheinland. I am sure, in real terms, Liberty would have really peeved with Bretonia for effectively helping keep Rheinlands Military going and vice versa.
'I would like to be half as clever as some people like to believe they are' Life is full of disappointments, it is how we handle them that helps to define us, as a person