Your question is tagged 'iPhone' so I am going to give an iOS-specific answer.
The offline storage, which holds the files linked to in your manifest, seems to be limited to 5MB. Evidence for this is all circumstantial, as the limit is not mentioned in Apple docs. However, some Apple engineers have conceded that there is a limit. The newest versions of Mobile Safari, in some circumstances, offer to allow the user to expand the storage, but you, as a developer, cannot force them to do so.
5MB is not really that much, and many users will certainly notice that something is going on, and if they don't want it to happen, simply close the tab. I understand that not every country has the same limits, but most users in the US are limited to 2GB/month. At this rate, an unsuspecting user would have to accidentally re-download your manifest, and the files it lists 100 times to use up just 25% of their bandwidth allotment. It's a fairly low limit, and the possibility of maliciously using up someone's data allotment is fairly remote.
As far as how to tell if a user is on 3G or WiFi, check out the Reachability example in the Apple Developer Center. It does exactly that. There is no way to do it in a web app (as opposed to a native app) that I am aware of.