Unlike everything else that can be applied to projectile weapons, augment crystals do not appear to have any rule that specifically transfers its effects to projectiles. By that fact alone, I’m more inclined to think of it as an oversight than an intentional limitation.
However, there are some things to note here.
One, many of the crystals either are melee-only (crystal of arcane steel, witchlight reservoir) or don’t care how the weapon attacks (crystal of adamant weaponry, crystal of illumination, crystal of return, crystal of security).
Two, it seems to me that the usual rule stating that magic on projectile weapons transfers to the projectile isn’t really necessary. After all, the remaining crystals all talk about “attacking,” “hitting,” or “damaging” creatures: how does a projectile weapon do these things? Through a projectile. A bow “attacks” when it shoots an arrow, “hits” when the arrow does, and “deals damage” by hitting you with an arrow.
That’s kind of a stretch by RAW, I know. Only a bit, but it is. The explicit statement everywhere else, but not here, seems to imply an exception. But applying such crystals to a projectile weapon would be useless if it didn’t transfer the effect to the projectile, and if that were what the rules meant, I’d expect the crystals to simply be restricted to melee weapons in the first place, which they aren’t.
Best Answer
Depending upon the effect, an intelligent item may be able grant the effect to its possessor, but, like an NPC, the intelligent item's not obligated to
Intelligent items have their own independent action economies, desires, and wills. Although an intelligent item will frequently use its powers on behalf of and at the behest of its owner, it can sometimes refuse.
Intelligent Items on Intelligent Item Powers says
Emphasis mine. This means, for example, that Snakebite, an intelligent item with the special ability true seeing at will, can, on its turn, take a standard action of its own to activate an effect like the spell true seeing on itself. Snakebite can then communicate what it sees because of that effect to its wielder via its telepathy. This has no more (and no less) game effect than if another creature communicates to the wielder what it sees.
Also, Snakebite possibly could, as this answer mentions, use the true seeing effect on its wielder, too, as true seeing has a Target entry of creature touched, if the GM determines that a creature touching Snakebite is the same as the sword being able to touch the creature. (That is, the effect's creator "must be able to see or touch the target," and while the sword can be touched to others, the GM must determine if this is the same as the sword being able to touch the target, lack of independent motion notwithstanding. Seriously, I think (hope!) most GMs would view a wielder touching another or himself with the sword as equivalent to the sword itself doing the touching, but it's wise to ask.)
Likewise, effects duplicating spells having entries of Range: Personal, Target: You, or both should, unless the GM rules otherwise, only affect the intelligent item rather than the wielder, sometimes with odd results (e.g. blink, mirror image) (This GM urges others not to distribute intelligent items with such special abilities unless the GM wants baffled players.)
However, Snakebite's special ability true seeing is a dedicated power, and dedicated powers are more restricted. Intelligent Items on Dedicated Powers says
So unless the wielder convinces Snakebite that there might be a serpentfolk under the effect of an invisibility spell Right now! Over there! it can refuse to use the true seeing at the wielder's command. (Were I GMing, I'd have Snakebite using its true seeing ability all the time but have the weapon relay only evidence relevant to serpentfolk without prompting, but I would also have Snakebite make Perry the Platypus noises yet call them mongoose noises. I expect your GM will vary?)
Before introducing intelligent items into the campaign I recommend that the GM make sure he's familiar with the host of rules associated with intelligent items. Adding an intelligent item to the campaign adds another NPC to the campaign world, and the GM must be prepared to play that often single-minded, emotionally stunted, and relentlessly demanding character.