When counting the red 3's left in a persons foot can he deduct the value of the red 3's from his black books?
No. The red three played to the table counts for the player (100 points). The red three in the player's foot count against the player (-100 points).
When adding the score, a 100 added to a -100 will cancel out, of course, but that shouldn't be confused with deducting the 100 from the penalty, lest you confuse that for leaving the player with no penalty and just the 100 points.
From the rules:
Red threes count 100 points toward your score if they are on the table and 100 points against your score if they are in hand.
If your opponents ‘go out’ (get rid of all their cards) before you have grabbed your ‘foot,’ and there is a red three present, that three counts against you.