I think we'll never find out how ned found out where she was. I think sometimes GRRM will leave it to the reader. It doesn't matter how he found her but that he did.I think its a little similar to the rhaegar/lyanna thing and whether she was kidnapped or not. In the end,the outcome would've been the same. I think it comes down to how much detail you want to give knowing that you already have 1300 pages written and do you really want to add more.
I think Varys' character on the show became a victim of the show beating the books. I think there's a lot more to what Varys is really up to or knows. I'm sure the books will have more to share because the show is so compressed fo tie everything together for a conclusion. So in the end I think they'll keep it short and simple on what Varys knew. I personally think Varys will die when the truth comes out about rhaegar/lyanna/jon. There's no way Varys didn't know rhaegar and lyanna were married. That's why I think there's still a lot we don't know what Varys' end game is