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Holy/Unholy Water are oddities, (and not in the sense of lets blame 3.5). Looking through the Alchemy Manual, it seems (unless I missed it), that neither are considered "alchemical items", and can not be crafted, and thus the only way to create them is by the Cleric Spell Bless or Curse Water, both of which are Aligned spells.
However, Holy Water, (and Unholy Water which seems to just use Holy Water as the base and is not described itself), is not actually an Aligned item. Or even a magical item. It does contain a lot of text that is highly suggestive that it is, but never specifies so, which is odd if that was the intent, because every other case I can think of, this is explicitly mentioned for the spell, item, feat, ability, etc. . .
So, as far as I can tell, Holy Water is not a [Good] Items, though Bless Water is a [Good] Spell. And similarly, Unholy Water is not an [Evil] Item, though Curse Water is an [Evil] Spell. Being that it seems these are the only ways to create the two items, (even Craft Alchemy doesn't mention <Un>Holy Water as an option), it does seem that this was intentional. Both Holy and Unholy Water are not included in either the Alchemy Manual or Adventure's Armory (Power Spell Components), but neither are also listed as Magical Items.
So, as far as I can tell, they are not either Aligned or Magical in nature, (outside of being created through a spell), and so would not ping for Detect Evil or Good, or even Detect Magic, which seems very intentional.
Part of this is that Paizo really mucked up Positive and Negative Energy, in the sense of making it very inconsistent in how it works, (Channel Energy either heals or harms based on both Creature Type and what application the user is intending, Align Channeling potentially uses Positive Energy to hurt Good Outsiders and heal Evil Outsiders if they want, etc. . .)
Positive Energy itself, and similarly with Negative Energy is NOT Good or Evil. Both are simply unaligned "spiritual" energies that are an intrinsic part of the universe and life. It is not the same thing as Sacred/Profane, Light/Darkness, Holy/Unholy, Divine, or even Neutral (with a capital "N") any more than "Fire" or "Bludgeoning" is. It just happens that generally speaking, Good aligned casters/beasties/options tend to use Positive Energy, and tend to use them for Good, while Evil ones tend to utilize Negative Energy more, and generally for at least NOT Good uses.