Are there any ways to increase the evolution pools of either of the hunters abilities
I don't believe so. You could always take the Evolved Companion feat to get them some extra (fixed) 1-pt evolutions, but that's it.
and how would the size increase evolutions interact with the animal companion, say if the animal companion were large or huge sized?
You'd think the archetype would spell that out somewhere, but it doesn't, so this is up to the GM to figure out. :-(
(Sorry not to be very useful... now you know why I didn't reply yesterday.)