BATTLE PLAN: If three or more Utility Belt Items are attached, assigned character can use Indomitable. If five or more Utility Belt Items are attached, you may give the assigned character a free action and select an opposing character within 10 squares and line of fire; that opposing character can't use team abilities until the beginning of your next turn.

Do Costumes count toward the highlighted part?

Quote the whole item...clearly Costume=/=Utility Belt Items

ninja speak wise

if a character already has indomitable, is it pointless to attach three or more items on the UB? I mean, how does countering Indom affect it if you have 1 vs 3 items attached to the belt?

More specifically, if I have three items attached to the UB assigned to my character who already has indom on the dial or has willpower, if an opponent counters willpower, will I still have it because the UB also grants it?

You can't use a game effect from more than one source, so if you have Indom or Willpower and 3 or more items on the belt that Indom from the belt is "dormant", for lack of a better term. However, if you lose the Indom/Willpower you possessed the belt-supplied use of Indom will go "active", so you are never without the effect.

Plus, the ability you get when you have 5 items attached is useful for everyone. If you have 5 items attached, you have 3 items by default.