My folding bike is not a Brompton, or even Brompton-like. And it doesn't fold.
But it has 20 inch tires. If you're riding on relatively smooth surfaces (paved roads), then I don't see any drawbacks to a smaller wheel. I guess some folks find them rougher when rolling over obstacles, but I haven't noticed that. In fact, due to some geometry issues of my bike plus the lower center of gravity, sometimes I prefer it when I know I'm heading for rougher than normal terrain.

Basically I find that my 700c bike feels faster and is definitely more comfortable on longer rides, but when actually timing my commute, the differences are minimal. I have a friend who tours on a small wheeled bike and likes it fine.

More than wheel size, I'd pay attention to geometry. I would definitely take that question to the folding forum. Just like full-sized bikes, folding bikes come with just about any kind of riding in mind, but, given their role in multi-modal travel, I think many of them are geared towards shorter, more relaxed rides. Mine, while able to haul a surprising amount and while incredibly comfortable over the short term, will never be a "zippy" bike, and the very upright position begins to wear on me after an hour or so in the saddle as I find there's very little ability to stretch or change position. But that's my bike. However I think a lot of folding bikes are made with short-term comfort as the priority, and for a lot of uses, that's perfect. But their are also faster folding bikes, touring folding bikes, etc.

If you want another resource for Brompton bikes, check out The Path Less Pedaled, where they are currently touring on Bromptons, which speaks well to their comfort and suitability over the long haul. They also post on BikeForums at times as well, so you may be able to hit them up with specific questions.