When a card (or cards) are accessed in the Research and Development stack, is this card revealed (to the Corp)? I'd say no, as I have not seen any mention of this in the rule book, but can anybody confirm this?
You are correct. The card is not revealed to the Corp.
Furthermore, can upgrades affect the runner, when obtained from the R&D stack when accessing it?
No, not usually. There are cards which explicitly state effects that occur when accessed from places other than Nodes. So unless the card says otherwise, nothing happens when the card is accessed from R&D.
I'm asking these questions because Sparky's "Run flowchart" says:
16. Runner: Run is now considered successful. Choose the order in which you want to access the cards there, including face-down cards.
17. Corp: Cards affect Runner in the order he or she chose. Any face-down cards are revealed.
Should point 17 really say something like "Installed cards affect..." and "Any installed face-down card..."?
You're right -- it should probably be slightly more clear. I do not believe this applies to R&D.