Not exactly.
You are right on the books.
The money is not physicaly there.
The money comes from the fact that, even if you don't count the books, you could throw a pebble in my home and it would land on an ancient, priceless artifact that I found in ruins around the world.
As for orphanages, I make a yearly donation to every existing hospital and orphanage in Equestria under a false name. I will not disclose how much I donate, because that would ruin the point of the fake name. The point is, Miss Lyra, I do good, but I do not need or want recognition. The good I do is reward enough.
But yes, I could effectively fund a small country for about ten years entirely on what I possess.

There are only two orphanages in Equestria. I know, because I’ve volunteered to both of them. There isn’t even one in Canterlot, let alone Ponyville. The good you do, the one that’s reward enough? Isn’t enough.

Think Celestia Scootaloo almost died, so that we could at least find out she has no where to go every night.