I can't provide a definitive answer, but I can provide more empirical evidence, and some justification, that the answer is NO. I have an app that uses SCNetworkReachabilityGetFlags to check whether a particular host is reachable (e.g.: www.mysite.com). Depending on that reachability check, it then uses [NSMutableData dataWithContentsOfURL:] to download the data.
The app has always worked fine, but recently I've been doing some coding at work where network access is via the corporate HTTP proxy. When running the app in the iOS Simulator (which uses the proxy settings configured on my Mac) the reachability check fails. At first I thought that perhaps the iOS Simulator wasn't using the Mac's proxy settings, but Mobile Safari in the simulator worked fine. So I removed the reachability check in my app and the call to [NSMutableData dataWithContentsOfURL:] worked fine. This would appear to indicate that SCNetworkReachability does not respect the proxy settings.
Having thought about it, this is probably the correct behaviour if you view SCNetworkReachability as running at the TCP/IP level, not at the HTTP level, in the same way that ping google.com on a Mac/PC behind a corporate firewall doesn't work either. The HTTP proxy (as the name implies) is for the HTTP protocol, not the whole TCP/IP stack.
Having read the answers to this question on Reachability I'm inclined to bin my reachability check altogether. Even though it's only been a problem in the simulator until now, it could be problematic in other situations (e.g. public WiFi hotspot that requires authentication).
