There probably is a slightly increased risk of something potentially going wrong just because of the way a stacked battery setup works. Theres a risk that you can overdischarge one of the
batteries more than the other and have an issue, but I personally think ECF and the internet made WAY too big a deal out of it. There's a lingering (albeit probably minuscule) danger of something bad happening with ANY rechargeable battery when you're drawing high currents off of it especially the way an ecigarette does. I'm sure someone else can explain the technical aspects of it better than I can though.
This is just my $.02 though, I still run stacked
batteries in all my PVs. Buzz is still running the original unprotected batteries in it, and I check them with a voltmeter every so often just to make sure they're still kosher. They're never more than .05v off of each other. I also make sure my batteries stay in pairs (i buy the two batteries at the same time so they're identical) and their positions get rotated every time I put them in.
Most of the time the stacked battery setup will give you superior performance to the single cell, although the single cell will usually run longer.