Did we ever get a reason why clones were being deleted? I was not able to find a post stating why.
I have mostly come to terms with my poor decision to not spend $5 (yes, there was a sale to clone for only $5) to clone my progress to era but would like to know why this option was not available to us in perpetuity.
I can’t say for certain if it was explicitly stated, but you can assume because it wasn’t profitable (most companies won’t kill off something profitable unless they need those resources elsewhere, but I don’t think there was that opportunity cost factoring into this decision). The cost to keep the servers running (maintenance/security updates, power bill, etc) was likely more than the how much was being brought in through the service being offered. I’d say the vast majority of the clones were probably done within the first few days of the service being available, with the next highest point being the sale after they stated the service was going away. All points in between were probably operated at a loss.
But who really knows? 
I’m not sure, but if I had to guess it would be due to data storage not being actually free, and potentially freeing up names.
After about a year of being able to pay for clones, and a pretty long time of them being only $5.00, they may not have anticipated a handful of people wanting to pay for clones at a future date. Or maybe the did the math and thought that it wasn’t worth the costs of keeping the snapshots.