I always use online check-in when it becomes available, and I can’t even recall the last time that I got a “surprise” upgrade during physical check-in. The upgraded room type always shows up in the app on the morning of arrival at latest (often earlier). If I don’t see an upgrade in the app, I reliably expect not to get one. So, it’s unrelated to actual arrival time.

Of course I don’t know whether the two things are related, but many properties seem to be doing things with the online check-in information (often, late check-out also gets confirmed in the app). It’s certainly worth trying if you haven’t been doing it.

Regarding welcome amenities etc., I haven’t noticed a pattern based on time of arrival either. It seems to depend more on the brand and specific property. Again, online check-in probably can’t hurt to let them know about your planned arrival time.