It's not paying double. Take the total number of instances serving the app and divide them across data centers and availability zones within datacenters. This might require adding a few of servers if the app is replicated across a very small number of instances, but for apps that already have a significant number of instances to handle the capacity, it's just a matter of rearranging things.
Depending on how quickly new instances of the app can be brought up to, it may be worthwhile to run a bit more capacity so that the remaining instances don't melt down should all the instances in one zone become unavailable.
Hardware will always fail at some point. You can either add extra resources elsewhere, or deal with that inevitable downtime. Both are reasonable, depending on the impact of downtime.
Depending on how quickly new instances of the app can be brought up to, it may be worthwhile to run a bit more capacity so that the remaining instances don't melt down should all the instances in one zone become unavailable.