I think there was a Xeon before that, but both in the same year. No doubt, back then HT was a different beast and required to do more code wise. For more recent software development, I don't think one has to do anything to take advantage of additional threads and HT. It works very well out of the box using "normal" processes and threads.
Have not seen that article, but yes. More and more security issues show up with HT. Those issues have always been there, it's just that nobody noticed until they opened a can of worms with Meltdown and Spectre. In the past, these sort of attacks have been on hardware (there's a somewhat recent CCC talk of hacking the Nintendo Switch by sniffing the eMMC bus among other things), but now it's software related where no physical access to the hardware is necessary. I don't think there's reason to panic yet, but wouldn't be surprised if more and more issues with HT are discovered in the next year of two. I found Intel not putting HT in their latest CPU a little concerning. Do they know something big that we don't yet? Of course HT can always be disabled, it's just one question that remains... is buying a HT CPU worth it now when down the road Apple, Microsoft, Linux might disable support? Personally, I'd probably go for an i7 in the Mini and if HT gets disables one day, just live with it.