Nope, it does alert you, plus if you miss it you get a missed Facetime notification just like you'd get a missed call notification.
[At least that's how it works on the iPhone, I've not tried it on my iPad but I don't see why it wouldn't do the same]
Once iOS 6 is out, people will also be able to Facetime you on the iPad via your phone number, instead of only via your Apple ID's associated email address (I assume Apple is simply going to allow people to also associate their number with their Apple ID).