If I have 7 runes and play siphoning strike on a vex apathetic in the battlefield, how much damage will it deal if I have to pay deflect which will bring me to 6 runes?

4 damage. The 7-rune check on Siphoning Strike is evaluated when the spell resolves, and by then the Deflect cost has already been paid — recycling a rune drops you to 6 runes on the board, so the "7 or more" condition fails.

The Deflect power cost is paid as part of playing the spell (Rule 356.2, 809.1.c), and a recycled rune returns to your Rune Deck (Rule 161.2.b), so you control 6 runes at resolution. Same timing rule as FAQ #11663: the 4-vs-7 number is a resolution-time condition, not a choice. The "channel 1 rune exhausted" clause on Siphoning Strike doesn't change this — it's separate and only matters if Vex actually dies.

Minor caveat: if you paid the Deflect cost from Power already sitting in your rune pool without recycling a rune, you'd still control 7 runes and it would deal 7 instead.