5000 does not necessarily mean its a big world, it depends on wether or not all these 5000 nodes are visible at all times.
There is a bit of overhead per node - although something I'm working on minimizing. If they are all visible on the screen at the same time, performance would be the biggest challenge.
If every node looks the same, InstancingNodes in the latest source of Balder is something that might be worth looking at for you. It has databinding capabilitiies and was built for faster ways of getting a lot of objects rendered. In the latest source you'll
find a InstancingNodes sample in the SampleBrowser as well that shows how to use it. It supports the event model in Balder, so every node fires mouse events as well, if that is something you'd need.
It sounds a bit to me that my suggestion of creating a container and rotate/scale it is not the way to go. But rather move the camera around, which brings you back to the flipping problem I guess - which I really don't have a good answer for you right now.
Another thing worth mentioning - there is something called PassiveMode, which is an option on the Game. With it, rendering will only occur if something changes. So if your model is for the most part just sitting there and you only need tooltips and such
when hovering over Nodes, PassiveMode is the way to go.
Also, every node has a Tooltip property, which lets you define the tooltip directly - the Silverlight TooltipService does not work with Balder nodes.