Yes.Me too. This is a real issue and you've described it well. I think it probably has something to do with the iPad's support for javascript and the way YouTube have implemented the buttons. Right now, the only way to 'reply' is use @username but that might not notify the user (as you mention).
Also, I cannot accept comments (only remove them). If I hit accept it shows a brief view of the reply button but goes back to accept and nothing else happens. I think this is where the buggy/clever javascript is.
I can't see there being a fix for this, it's Google not coding to the iPad's standards (and Apple won't change that I don't think) I'll have a good look though and report back if I find a solution, at the moment this is the top hit on Google though.