These numbers are useful proxies for how likely you are to have your work disrupted outside of your own control.

If you do something 100 times a day against a four-nines service, you can reasonably expect that everything will succeed.

If you do something 10,000 times a day against a two-nines service, you can expect to hit a substantial number of errors during that day, or even have long periods where your work cannot happen at all.

People aren't frustrated with Github because Github has 98% uptime or whatever the specific number is. They're frustrated because it regularly interferes with their ability to work. The 98% number is just a concise way to say it.