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I agree, that this will probably not affect the use of the Cloud, though it is every person's responsibility to do due diligence in understanding who the vendor is, the services offered, and security used.
In the short-term, cloud services should be used as backup, not main data, and unless you are not 100% comfortable with the vendor, do not use the cloud for sensitive data, whether encrypted or not.
Probably not, although it may reinforce the idea that the only copy of data should not exist only with one cloud storage provider. A business who cannot afford to pay for a private cloud would be prudent to spend some money for multiple cloud providers, even if there is residence from the "bean counters" to spending twice for the same thing. Asking them to quantify the monetary cost if all of your data is lost usually helps move that conversation along, plus the cost isn't really all that much.
It would be helpful if there were uniform international regulations on data ownership, so that you could rest easy knowing that even in the event of a problem with the provider, you could retrieve your data. Larger companies are probably going to deal with this by going the Hadoop route and establishing private clouds.
Lastly, a point specifically about Megaupload; I can't imagine many (if any) business choosing to use a provider that is focused on file sharing for cloud storage. Much more likely is a choice of someone like Amazon, where you can feel pretty confident there isn't going to be a multi-national police action against your provider.