Usually side-by-side colonies are used as nucs. They overwinter well that way, and like any nuc you can take resources from them to give to production colonies, or replace losses.
But yeah, if you throw a queen excluder and some supers on top, then sure, they'll store honey. But I think few if any commercial operations use two-colony hives for the bulk of their honey production. I think the main reasons are just minor management hassles compared to standard hives.
For example, Ian Steppler in Canada runs some 3-colony hives. It's basically 3 nucs on bottom, then two stacks of 10-frame supers, with a layer of queen excluders in between. Seems to work great, but it's not like he's switched his whole operation to that setup. I think it's more like a way to keep his nucs from swarming and get some honey to boot.
As a beginning backyard beekeeper I've run some double nucs, and sometimes supered them when they were growing out of control. It worked fine, but I think ideally I'd pull resources more aggressively and not need to super.