Well, you can't ever get more than 16 cards on top of your deck (if you cast 4 Transcendence and 4 spells all in once turn), and your chance of being able to get enough quanta and then refill your hand in time to do that before you've drawn at least 16 cards is pretty much nil, so I'm not really worried about it.
The only card that I'd be worried about overduplicating via Transcendence is Shard of Divinity --- I gotta admit, casting 4 SoDs and stacking your deck with 16 more sounds pretty brutal -- until you realize that you then have to go for 8 turns without drawing anything but SoD, and your opponent can probably catch up with your HP gain by then.