The number of hands is the total number of hands, not the filtered number - that would get a bit circular and cause no end of problems.
You could create a new custom statistic for number of non-heads up hands by duplicating the Hands stat and creating a new column to only count hands where there were more than 2 players; then you could filter on that stat instead.
(Actually, you only need to create the column unless you want to display the hand count - you can filter on columns directly.)
Have a look at the
Custom Stats guide and the
Custom Statistics and Reports FAQ.
You will need the database field: holdem_hand_summary.cnt_players
If you get stuck, please post back and we'll help you out.