The 5mb limit applies only to WebStorage I think, although iOS and some other platforms may prompt if you store "a lot" (25mb+ ish). Usually the user just needs to OK it and it will run.
IE10 supports the app cache, but IE9 doesn't, which is a bit annoying. It should still load most resources from the normal cache, but it might re-download in future if its cache expires. App cache fixes that and IE10 should work fine.