Sounds right to me. The Spellcraft to identify the spell is exactly as it should be in the skill's rules, and Nondetection is a correct precaution to take for a sufficiently paranoid wizard, especially after getting confirmation that someone is out to get you. You waited a day, so he definitely would have had time to prepare and cast a Nondetection or two. It'sa 3rd-level spell that lasts 1 hour/level, so at the level you're at it'll only take 2-3 castings per day for total coverage, or just 1-2 with Extend Spell or a Lesser Metamagic Extend Rod, and it shouldn't overly tax his spell reserves in doing so.
To work around it, you could try to brute force your way through with caster level buffs and repeated castings. If Nondetection is blocking the spell, the save doesn't even come up, so Scrying's 24 hour lockout won't apply. That said, it might still take a lot of tries and/or a lot of power boosts to get through.
You may have better luck with alternative information-gathering methods. Contact Other Plane, Augury, and Divination should still be able to give you information if you ask the right questions, regardless of how powerful the Nondetection is (it only protects against detection). You can attempt to scry on someone else in the vampire's retinue instead of the big bad himself (assuming you can get a sufficient connection); it's unlikely that he'll have enough spells for everybody. The Gather Information skill is rather mediocre, but it doesn't require training so you might still eke out a little useful info with it, especially with skill-buffing spells to enhance it.
Is there any specific sort of information that you were hoping to get via scrying? It might help narrow down the alternative methods to get it.