If I have 7 runes and play siphoning strike on a vex apathetic in the battlefield, how much damage will it deal?

7 damage. Siphoning Strike deals 4, but "if you control 7 or more runes, deal 7 to it instead" — and that check is evaluated at resolution, so with 7 runes it hits Vex for 7 (FAQ #11663).

Vex's stun ability doesn't factor in — it only triggers when an opponent plays a unit, and Siphoning Strike is a spell. One cost note: Vex's Deflect makes spells targeting her cost 1 extra Power (any domain) as a mandatory additional cost (Rule 809), so be ready to pay that — but it doesn't change how much damage the spell deals.