The physical ark of the covenant, as written within the bible, has a description that sounds far from "ugly". The ark itself was a chest, carved of fine wood and inlaid with gold. Inside of the Ark were the tablets of the Ten Commandments, a jar of manna, and Aaron's Rod that budded (Heb. 9:4). It served as the symbol of the very presence of God. To capriciously look within it, as a mere object of curiosity, would have been an act of disrespect to God himself then and the reasoning for divine retribution.
All of that being said, I would say that the phrase "looking at D3D v3 code is like staring into the Ark of the Covenant" is only a reference to the speaker's self-assessment that he suffered and metaphorically died trying to read it.
As stated by Cargill, it appears to be nothing more than an over the top expression.