Imagine I'm on hacker news and there's someone on mastodon I think someone should follow and their mastodon handle is @cooldude@cooldude.example.com (because they are so cool they run their own instance).

You definitely can't click that handle and add follow them, I could put https://cooldude.example.com/@cooldude and you could click to their profile on their instance, but there would be no way to follow them directly from there on your mastodon.social (or whatever) account, you have to go to your instance and type/paste in their handle and then click follow.

Edit: There is a remote-follow workflow that involves clicking a link and entering your full handle to get redirected to a page where you can follow them. Maybe slightly better, but still not great.