The entity that they sue pays, if they win.
So, who do you think that they can sue and on what grounds?
The MPAA didn't shut down their company or arrest them and doesn't have the power to decide whether someone else will do those things, so it will be extremely difficult to hold them liable.
Prosecutors and police are almost never liable.
In such case, the government would pay (but not the individual prosecutors, as they are acting merely as agents of the government). Damages would be based on economic harm actually proved, i.e., lost business from cancelled customer contracts, lost ad revenue, etc. Future growth potential is not taken into account for damages purposes.
However, note that MegaUpload did not follow the DMCA. Its entire business plan was based on committing illegal activities, and was designed from the outset to maximize the revenue generated by such activities over the revenue generated by the potential legitimate uses of its services.
If you want a role model to follow in the media distribution market, look to BitTorrent.
I mean... it seems the company is dead. Can they sue for damages? And if so who pays? Do the courts recognize things like growth potential when they value lost damages, and do they look at profits or just revenue? The reason I ask is because I'm curisou what would happen if this were a smaller startup that was strategically minimizing profits and perhaps even revenues in order to aim for growth.