When I checked in at Kota Kinabalu 63 Hotel in Malaysia, I left out a person's check-in name. It shouldn't matter. In addition,

Don't say much when you check in, just go to the counter alone. If you only give him a meal voucher, tell him it's two adults (just book a double room or a big bed room). If breakfast is included, taking the children directly to the restaurant may make you pay an extra child's breakfast.