Girls
Right, I don't think anything ending in "a" will work with Hanna, so if you're really set on using Hanna for a middle name, then I wouldn't go with Matilda or Isabella, even though they're both nice names (I liked Matilda for my DD but it was too similar to a close friend's daughter).
Phoebe definitely sounds nice with Hanna!
Boys
I like all of your boy's names! Samuel/Sam is one of my very favourites, and Angus is nice too (but I don't especially like Gus). Probably wouldn't choose Joshua or Jacob myself just because they are a little too popular, but they're still nice.