I'm not sure, but when you stack 2 18350's, they will generate the same mAh as one of them (800 mAh vs 1600), but with double the volt (ie 8.4 instead of 4.2). I don't know what this does to vape time though, because the 8.4 gets regulated down to a more useable voltage.
I remember back when I was into hobby grade rc cars, and the standard battery packs were 6 cells. There were several 7-cell packs that gave you a bit of a power boost, and there was always an argument over whether 7 cell packs lasted longer or shorter than 6 cell packs. I remember there were quite long discussions, people using a fixed drain to test runtimes for 6 and 7 cell packs, that sort of thing.
The consensus was that more cells do not increase runtime. The simple difference between series and parallel would support this. If you have stacked 18350s, you are getting roughly 8.4 volts when fresh off the charger. If you run them in parallel you double the capacity. It would violate some laws I'm sure if stacking batteries doubled the voltage AND the capacity. Parallel only doubles the capacity, series isn't some magical setup that allows you to double your capacity AND voltage.
So I'm pretty sure your right, stacking batteries does not increase capacity. Although like you said, the regulation of a pv could possibly effect actual useable vape time with the batteries. An 18650 getting boosted could be different than stacked 350s being regulated down. Another thing to think of is voltage drop. When a single battery starts getting around 3.4v or so most of the cheaper devices have trouble boosting them well. You might notice this as a drop in power, and charge your batteries up earlier. Where as with dual 350s, the voltage doesn't need to be boosted, and stacked 350s totally drained still give more than enough power to supply your vaping needs, meaning you can take each cell down to a lower voltage before needing to recharge, which effectively increases your capacity.
So stacked 800mAh 350s do not actually give you 1600mah. But it's likely that stacked 18350s could last longer than a single 350 in useable vape time. So stacked 350s could give you more usable vape time than their single mAh rating would suggest, but still nowhere near double their rated capacity.