I would say be respectful of people's time. Rank your reference people from the most desirable to least, then ask from the top. If you need 3, ask the top 3, and if any of them declines, ask the next best one. If you don't have all 3 by a certain time, also start asking the next best one. If you are in a time crunch and very risk-adverse, asking 1 more than what you need is also understandable.
Is it appropriate to approach all (or more than enough) potential
referees, in the first place, in one go?
Don't do that in one go. Most of your reference people probably know each other and if they found out you're using a flooding approach they may decide not to write one because they may think someone else will be writing one.
Should I keep them (those whose letters I did not use) updated? And if
needed, how does one politely do so?
Not necessary. That kind of update will only bring bad flavor, as you're telling them that i) I consider someone else's words a lot more valuable than yours and ii) I just wasted your time.
Most application processes (at least in the US) are online now. If you have gathered more than what you need, you can check with the school if you can submit them all or have to drop some. My belief is that the schools do not follow up with the writers of the reference letter. I have never received any follow up on my letters after I submitted them through the system.
So, some safety measures is fine but don't overdo it. And remember to thank everyone who wrote a letter for you. And if you do get accepted, inform and thank them all as if you have used all their letters.