I ride the Golden Gate Bridge to and from work all year long. Last year I rode a Litespeed Tuscany with Mavic Cosmic Carbones. I now ride a Look 565 with Zipp 404s. I weigh 140.
I say buy the wheels you like. Yes, there are particularly windy days when it blows like a tornado around the pillars on the bridge, but I can honestly say that that's the only wind that will bother you -- and it's not the aero wheels that cause the difficulty. Truthfully, riding with 404s is no big deal in just about any wind. And, I think it's clear that these wheels are flat out faster than non-aero wheels in any type of wind. Take a look at what people ride in Kona during the Ironman World Championships. If it's really windy they put 404s (or similar depth wheel) on the bike.