While I think that Helena is the archetypical Ravenclaw as Tim so nicely put it, there's no reason she couldn't have been placed into Ravenclaw simply because it was her mother's house. The sorting hat was created by the Founders to sort students after they were gone. In my imagination, at least, there would have been a good deal of time when the Founders would decided among themselves which students would be taught by whom.
In regards to the whole Salazar/Godric thing, I have two main points: first off, probably neither. That's the sort of canon fact that is relevent. I really think JKR would have mentioned something. However, it's fun to speculate on shipping between the Founders, and this is fanfiction, so go ahead and pick one of the men, but bear in mind my second point. People are not carbon copies of their parents. Just because Helena acts proud and sneaky doesn't mean she can't be Godric's daughter. I act very little like my own father, and I believe Dumbledore spends a good deal of time reminding Snape of this very idea in regards to Harry, James and Lily.
Then, of course, there's cmwinters' point, which I'm not going to completely repeat. Just remember that the Founders were probably a lot more three-dimensional than your average fic gives them credit for.