http://en.wikipedia.org/wiki/Corpus_Juris_Civilis
If you want to appeal to authority rather than answer the question, pretty much any Roman emperor makes an odd choice.
But here, Justinian's argument is given. Seas and rivers are part of the commonwealth, so nobody should be denied access.
In any case, if there is some principle underlying Justinian's edict, what is it? How did he determine that the sea is part of the "commonwealth", but that a mountain or someone's house is not? This is hardly explained in the given quote.
In short, seas were part of the commonwealth because Justinian said so. An <ahem> appeal to authority. But an appeal that Justinian made, not benjohnson.
That we continue to accept some historical precedents as good, but have discarded others is not at all odd, and does not invalidate the historical importance placed on access to waterways just because the same people also had lots of ideas we consider idiotic today.
A long historical precedent is however sufficient to explain it's modern day existence, which is what happened here.
You appear to have an uncanny ability to read far more into messages than what were intended.