If you've only had her two days then yes it is better to let her settle in. It's usually recommended to not clean them out or change anything for the first two weeks while they're settling in. I think they can like the penthouse
But it does make for more cleaning. If she does start nesting in the tubes though it would be best to remove those and the penthouse. The other thing to keep an eye on is how big she gets. Some hamsters can actually get stuck in the tubes - especially if they have full pouches. And some hamsters can grow really large!