1) Yes, submissions are manipulated, but due to the flagging mechanic, any bad submission with vote manipulation will be shot down. It's worth noting that public vote manipulation on HN (https://twitter.com/search?q=https%3A%2F%2Fnews.ycombinator....) is far, far less worse than the meritocracy known as Product Hunt (https://twitter.com/search?f=realtime&q=product%20hunt%20upv...), which doesn't penalize spamming people for upvotes.
2) Using startup-esque techniques like Recommended Articles and Verified users won't work, as it will kill the simplicity of HN (note that Reddit has tried similar systems not too much success). Content is the most important factor to determining upvotes.
3) Yes, there are a few articles by YC alumni over the years which receive suspicious amounts of upvotes, and I'm disappointed by that. (case in point, see the cofounder of ReelSurfer's submission history: https://news.ycombinator.com/submitted?id=njoglekar)