Most end up around 1/4" deeper so not a huge amount, whereas an NL-00 is around 3/4" deeper than you'd expect a normal 00.
If you wanted a significant amount of extra depth you'd need to ask for it.
The implications of extra depth are a slightly slower response and, as you mentioned, a deeper, lower, air resonance. It's only an advantage if that's what you want. If that's not what you want, then it's a disadvantage.
It might make sense on an OM and in fact I've done so (although it had a soundport which counteracts the deeper resonance, so it was a pleasant oddball), but I'm not sure if I'd suggest it for the SJ, since the SJ has a slightly larger soundhole than the OM which raises the main air resonance. So with a deeper body on the SJ you would be counteracting one of the subtle differences that separates the two models.
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