Yes, the API that you linked will be retired.
Google will not be providing a replacement product. Your transition will consist of either swapping Checkout with a non-Google provider or integrating Google Wallet Instant Buy or Google Wallet for digital goods. You will need to see which of the three can fit your checkout/payments model.
The API that you linked was Checkout's subscription capability. Google Wallet for digital goods supports subscriptions so you may want to take a look at that.
This page contains a lot of really good detail regarding Checkout retirement. I think it can answer all/most of your questions.
And yes, I do agree the entire ecosystem of documentation around the various Google payment related services is more confusing than need be. :)