A player signed up for cash and didn't show up. Do I still pay commission for him?

Yes. A cash spot stays counted, so the 7% (minimum $0.30) commission for it is charged even if you mark him “Didn’t show”.

You can mark it and add a fine: tap the player, “Manage participance details”, “Didn’t show”, pick a fine of 0 or 5 to 100% of the spot price (the price after any promo code or Early Bird discount, so a cheaper spot gives a smaller fine), “Save”. The fine becomes his debt to you; until he pays it he can’t join your games. The mark is available from the scheduled start until results are confirmed, or 3 days after the game if no matches were recorded. Choosing “In game” again undoes it.