Why skarner Q don't apply On hit effects

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read the wiki, his q applies onhit to first target only

"Crystal Slash is a point blank area of effect ability with a self-buff component.

Applies spell effects as an area of effect ability.
    Hextech Revolver item.png Spell vamp is reduced to one-third effectiveness.
    Rylai's Crystal Scepter item.png Rylai's Crystal Scepter will apply a 15% slow. 
Magic damage will be mitigated by magic shields.
Banshee's Veil item.png Spell shields will block the damage but do not prevent Skarner from gaining the bonus attack speed.

Additional Information:

Crystal Slash has no cast time and does not interrupt Skarner's previous orders."

Read the wiki, his q does not apply on hit effects to any target because it isn't a targeted ability. He can use it whenever he wants while scuttling around.

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what determines the main target? the last auto attacked target? why not just use auto attacks then?

There is no main target, as Skarner's Q is not a targeted ability. Technically speaking, he IS the target as it's an AoE around himself.