Yes, the included time from your copy of City of Villains will be applied to your existing City of Heroes account, as long as you use the UPGRADE button to apply the City of Villains serial code to your City of Heroes account on your PlayNC Master Account.

The reverse is also true - if you have City of Villains and purchase City of Heroes, the 30 days included with City of Heroes will be applied to your existing City of Villains account, as long as you use the UPGRADE button to apply the City of Heroes serial code to your City of Villains account on your PlayNC Master Account.