The Org level call https://developer.cisco.com/meraki/api-v1/#!get-network-appliance-uplinks-usage-history however states that "if more than one device was active during the specified timespan, then the sent and received bytes will be aggregated by interface."
You are mixing up the calls, this usage-history call does not say interfaces will be aggregated (it is the usage-by-network call that may do that.)
https://developer.cisco.com/meraki/api-v1/get-network-appliance-uplinks-usage-history/ gives the data for each interface separately.
2. Yes you can calculate bps that way.
But using the https://developer.cisco.com/meraki/api/get-network-appliance-traffic-shaping-uplink-bandwidth/ call is problematic unless you have a guaranteed throughput on the WAN circuit and are consistently/accurately setting the limits on each interface. But on a cellular or typical ISP connection, you will not have a guaranteed fixed bandwidth, so you cannot rely on this method.
Another factor is that the highest resolution is 60 seconds, the throughput in that 60 seconds could be, say, 50Mbps, and your link speed 100Mbps, however if traffic is bursty you may be hitting the link speed limit many times in the 60 second period resulting in application performance issues even though it looks like you are only using 50% of capacity.
I would also look at loss and latency as it may give a better perspective https://developer.cisco.com/meraki/api-v1/get-device-loss-and-latency-history/ you need to call this for each interface on a device.
3.
If your sites are single WAN connection, you could use this to infer WAN availability https://developer.cisco.com/meraki/api-v1/get-organization-devices-availabilities-change-history/
Chances are if a device is unavailable it's the WAN, but ultimately you still would need to do some manual mitigation to exclude cases where you know it was the MX or some other issue.
In a multi-link environment maybe you could use https://developer.cisco.com/meraki/api-v1/get-organization-appliance-uplink-statuses/ but this requires you to poll, there's no history available,