OK I'VE KIND OF HAD IT WITH THIS DISCUSSION! Learn to read between the lines, people!
First of all, if the interview did actually happen and the information on the source is true, then Kaz Hirai did not take a direct stab at the Nintendo 3DS. I know this because of two things:
a) He says that by Sony's own research (and we assume that he's not talking about a research that also takes into account rival products' technology. If the opposite to my prior sentence were true, then it'd be impossible to determine his intentions without further detail), naked eye 3D technology on portables is imprecise. This does not equal to: He says naked eye 3D technology on portables is imprecise.
b) He claims he has not seen the Nintendo 3DS. However, bear in mind this does not support point a) as much as it's a disclaimer, because he not seeing the Nintendo 3DS does not mean Sony's research didn't or viceversa. Therefore, point b) does not mean Sony's research excepts Nintendo 3DS technology. Point b) is actually useless in the most strict objective way of analyzing the information given.
So we see that point a) alone disacredits the claim of a direct stab, and point b) serves only as a further detail that he hasn't tried the Nintendo 3DS out.
Secondly, this doesn't mean that he didn't take an ocult stab at Nintendo's recently shown hardware. My personal, opinionated way of looking at it is that he did. I show my reasons for taking such stance:
1. He talks about negative results of the precision of a technology widely known to be exploited by a rival product, shortly after the showcasing of said product. He has very little reason to do so but to make people less secure about the quality of the product.
2. The 3D technology used for games for the PS3 is certainly different than that used with the Nintendo 3DS. By showing that, according to Sony's own research, naked eye 3D technology for portables is imprecise while at the same time speaking well of their own, different use of 3D technology, means to me (and that's where people could objectively say that it doesn't neccessarily mean anything, but alas, when giving an opinion, a little subjectivity must kick in, because otherwise it'd be a fact) that he believes PS3 3D technology for games will be the better one on the market in the forseeable future, inmediately meaning that all other 3D technologies for similar purposes are worse than PS3's.
And that's THAT. You can take sides on the implied meanings, but that's subjective and therefore you won't ever convince all other reasonable people. Strictly objectively speaking, he did not bash the Nintendo 3DS.