If there are any specific places where Deno didn't support a node API, please file a bug -- we definitely shoot for as close to node.js as possible, and if you have to modify your code that's most often on us.
No, I wrote my service some time ago (basically GitHub Webhook which does some crypto to validate payload and invokes kubectl) using Deno API and few months ago I took some time to update dependencies but found out that with new standard library version some APIs are either deprecated or removed, I don't really remember, but I felt the need to rewrite it.
Don't take it as a criticism, I totally understand that you need to iterate on API and nobody promised me that it'd be stable till the end of time, but still work is work.
https://github.com/denoland/deno/issues is the ideal place -- we try to triage all incoming issues, the more specific the repro the easier it is to address but we will take a look at everything that comes in.
(I'm a deno core dev)