There is definitely some overhead with function nodes. I think it all depends on what the flow is actually doing, how many messages you push through, how many flows you have and what you do in the function itself. I think in the big scheme, the number of function nodes are always less than the other nodes you use. But technically and bottom line, you will get the biggest bang for the buck if you use built-in nodes instead of function nodes.
Here is an interesting article about that topic:
https://groups.google.com/forum/#!topic/node-red/v6luhAc1kKU
EDIT: Something to keep in mind.. If I need 10 builtin nodes to represent what I can do in a "simple" function node, I might not achieve any performance improvement. Again, to me, apply common sense... If a single builtin node can do what a single function node can do, go with the builtin node.
