Diane,
As far as I know ereaders do not read column-count correctly, though I have not extensively tested this in awhile, but considering industry software such as KindleGen v2.9 has not updated since 2014, I doubt the correct support for it has been added to any current ereader. I say that because thinking of how you have to apply the CSS for two-column, you really can’t add it to the <p> tags or only the paragraphs individually will split to two columns and make the book very much harder to read, so you have to add it to the body tag or a parent div/section tag which the ereader would then treat all the paragraphs and headings equally and split the entire document in half (as it does in a browser) as there is no way to specify that the CSS only break the text to the bounds of the current screen.
I quickly tested column-count:2; on the <body> tag and then retested on the <section> tag in a recent book, and ADE doesnt appear to support it and neither does iBooks for Mac. I would try it on Kindle but most have a very small screen as it is and dont think it would be wort it (I mean unless you and your readers are still rocking the Kindle DX, but even that wouldnt support modern CSS such as column-count). Personally I think two-column on an e-ink ereader would be more distracting than anything (we always need to keep in mind how things that we do affect the readability of the material, not just how it looks on screen), and while I know this might not match your print book, it’s really not necessary when reading on an ereader.
That said, I havent tried flexbox and really dont have time at the moment to do so, but if you would like to test it and share you’re results I would be very interested to hear if it works or not.
Aaron