If a customer brings in cash, deposits it into his/her account and then immediately wires it out, should the amount of that wire be included in the Aggregation of Currency Transactions Report?

No - the wire is not currency.

But wouldn't that be a good way to launder money? The customer could deposit $20,000 and immediately wire it out and it now looks legitimate. Also, it won't require a CTR since it's not considered a cash transaction.

You need a CTR for the $20,000 - you said: "should the amount of that wire be included in the Aggregation of Currency Transactions Report". I guess I misunderstood.

May be something you file a SAR on. I would watch the account/customer and apply CDD/EDD procedures.