The cable isn't a mystery, the article states, but its fate was. Also, the cable's not in Cuba -- It was laid in 2007 between Cuba and Venezuela. They just activated this undersea internet link, and the real mystery is 'how's it misconfigured?' Slightly misleading title.
The article implies that the cubans are, for some reason, receiving packets over fiber, but sending over satellite, which, for all intents and purposes, is insane. It is a real mystery as to why anyone would configure a network to operate in this manner.
It is akin to having a 10gigabit fiber line in your office and choosing to have all outbound traffic routed over a 1.5megabit DSL line instead. Madness!
It's more like having a 10gigabit fiber line and choosing to have outbound traffic routed via carrier pigeon. It's latency, not bandwidth, that makes a satellite connection maddening.
Yes, that configuration is madness, but it's no mystery. The mystery is why is that configuration in use? The answer probably has to do with reducing internet usage in Cuba to prevent a Cuban Spring.
The most likely explanation is that traffic is bi-directional on the fiber line, but a lot of additional latency is introduced by software based (as opposed to hardware accelerated) deep packet inspection.