Oh, you are right, jury nullification is no more or less than the statement that a jury can acquit a defendant for any reason they damn well please and there's nothing to stop them; this is obvious to anybody that ever paid a lick of attention in 8th-grade civics class. I would hope it would only be used to refuse to convict under illegal laws, because otherwise it turns the concept of us being a nation of laws, and not men, on it's head. If a prosecution produces an unpleasant result under the law, but the prosecution is still legal, there are means (however imperfect) for the law to be changed. The jury deciding on their own that they like the defendant too much for his/her sentence is not how the law is supposed to work.
And not that your other points have anything to do with nullification, but...
The "see no evil" defense is pretty weak sauce against these money-laundering related charges. (And certainly they will get you civilly fined to kingdom come.) The idea that DPR/Ulbricht did NOT know the primary use of his market was the illegal drug trade is ludicrous in the extreme; it does not take any great leap of logic to discard such an assertion utterly.
And no, pre-paid providers do NOT benefit from burner phones. Such phones are usually subsidized at retail (plus there are real costs involved with activation) and when they are quickly discarded after a short period of time, so the provider takes it in the proverbial shorts. (But what do cell phone providers have to do with the proverbial price of tea in China? Not sure what you are getting at there.)
And, given that the police don't even need to file charges to perform civil forfeiture (I certainly usually don't agree with that practice), arguing that that was their motive for prosecuting him is also pretty silly. (However, in this case, civil forfeiture actually makes sense since nobody ever laid official claim to Silk Road's Bitcoins.)