A copy of a spell can be countered like any other spell, but it must be countered individually. Countering a spell with gravestorm won't affect the copies.

The triggered ability that creates the copies can itself be countered by anything that can counter a triggered ability. If it is countered, no copies will be put onto the stack.

The copies of Ominous Harvest created by its gravestorm ability are created on the stack, so they're not cast and won't cause abilities that trigger when a player casts a spell to trigger.

You may choose new targets for any of the copies. You can make different choices for each copy.

Gravestorm counts all permanents put into graveyards from the battlefield this turn. It doesn't matter who controlled those permanents, who owns them, or whether or not they were tokens.