IE9's global share is 2.13% and 3.84% in the US. It's 2.38% for the sites I'm supporting.

Here's the simple answer for supporting old IE: http://dowebsitesneedtolookexactlythesameineverybrowser.com/

But to be more precise, graceful degradation is the answer. I'm building an interface that needs to last for several years, and IE9 is circling the drain. I can't justify making too many decisions around browsers that will be gone soon at the expense of the experience in all the browsers that fully support modern properties now.

IE 8 and 9 will get a degraded experience, but the content will all still be there, and it will look pretty good. But it won't look exactly the same.

Depending on your industry, IE is still a major player.

But people should be more worried about how it looks on a mobile device, at least 50% of our clients traffic are from mobile devices now a days...

That's correct. The plan for IE 8 and 9 when I'm building heavily with flexbox will be for them to resemble the mobile breakpoints of the site. Since we build mobile-first, they'll pick most of this up without any extra work.