I was using an older non-public API which broke and am now using the public one. All is well. However, my pricing calcs are weighted to prevent someone from easily manipulating the profitability calcs (as was stated in that article at
https://bitcointalk.org/index.php?topic=220884.0). I am working on breaking down my charts between normal volume and low volume currencies for readability.
But, yes, if I have an issue getting a price, the coin disappears. So if an exchange goes down, and it is only listed on one exchange, the coin goes away.