Reddit's API can't access their chat system, doesn't work well with their search function, and (like with their own web client) can't easily collect all of the comments from a long thread. Also, I expect they will eventually cripple it further or shut it down completely, like Twitter did.
Representing threaded comments through an API is often implemented terribly. HN's API in that regard is absolutely bonkers. Lobsters probably has the most convenient API, returning the full comment tree in the response. As long as you're willing to do a bit of tree traversal, the Reddit API is fine.
I also don't really think Reddit will be dropping API support any time soon. There's been no indications in that direction except for a change in the unauthenticated rate limit that was made a couple years back.
