From the link you posted (emphasis mine):
Adobe® Flash® Player is the world's most pervasive software platform, used by over 2 million professionals and reaching 99% of Internet-enabled desktops in mature markets as well as a wide range of devices.
A wide range of devices do exclude iSteve mobile devices and a few others.
And if we also need support on iphone, ipad and blackberry for our website/web applications, then should we never use flash?
As for never, it's a question only S.teve can answer :)
You added an accessibility tag (and asked many related questions before), so let me answer from this point of view: your website should work with or without Javascript and with or without Flash, a PDF reader, MS Office, Silverlight, with or without a mouse, images, CSS, etc
Usability will suffer from the lack of JS but your website should still work and no information should be hidden and no task should be impossible to realize: it's called graceful degradation I believe.
Flash
Flash objects should be accessible, Adobe has a section of its site dedicated to accessibility. The object element should have an alternative at the end of object or nearby, this alternative can be another object nested and have its own alternative, etc but the last alternative should be accessible (a text, an image with alt or an HTML page). You can read about WCAG 2.0 techniques G58: Placing a link to the alternative for time-based media immediately next to the non-text content, G69: Providing an alternative for time based media and many others.
JS
I've used NoScript
for a long time and have seen more than often a common failure: using Javascript to detect Flash. That won't help.
Another one is the meaningless alternative "Get the Flash player at Adobe website". Yeah thanks, it's running fine, the only problem is with the detection script that won't run ...
So don't try to detect Flash, just put it in an object element and provide (a) meaningful alternative(s).
That will address both the 97% and 99% users, both the remaining 3% and 1% ones as well as, finally, those with Flash installed but who can only guess what unlabeled buttons in the SWF can do or worse get trapped in the Flash object while tabulating. These are blind users for the former and blind users as well as keyboard-only surfers for the second part.
From a recent survey, 75% of blind users keep JS running and it's unspecified for partially sighted people (probably more, keeping in mind that there are 10 times more partially sighted than blind people).