As others have said, that seem rather unfair to players, who accumulated a big stack. The most fair would be to use the ICM model and calculate the ICM value of each stack, which is often the method used for deal making at final tables. However that might cause confusion among players, who dont know, what ICM is, and I guess, this is why, most sites use some kind of approximation to the ICM model. If players are already in the money, then the easiest solutino is to pay out, whatever they already looked up, and then distributed the rest based on chips. So for instance 1M chips in play, 1.000$ to still be distributed = each 1.000 chips is worth 1$.
But as others have said, this dont happen very often at all, so if the model is slightly unfair to big stacks or small stacks, you can just consider it another kind of "bad beat", when you end up on the losing side. For me the far more important aspect is, that sites do actually cancel and refund, rather than let players wait for hours to see, if action is eventually resumed. My last server crash was on ACR, and I think, action was halted for more than an hour. And this I actually find very annoying, particularly since I was playing SnGs. Maybe its ok to put a slow MTT on hold for 80 minutes, because people playing those have signed up for a long ride. But SnGs are supposed to be over in somewhere between 20-90 minutes depending on the format. So for those games I really feel, that if action has to be halted for more than 15-20 minutes, they should just be cancelled, so that people can move on and do something else.