You have to use the ReconfigVM_Task method from the SDK for that.

$VMname = <VMname>
$vmImpl = Get-VM $VMname
$vm = $vmImpl | Get-View

$spec = new-object VMware.Vim.VirtualMachineConfigSpec

foreach($dev in $vm.Config.Hardware.Device){
  if($dev.DeviceInfo.Label -like "Serial Port*"){
	$temp = New-Object VMware.Vim.VirtualDeviceConfigSpec
	$temp.device = [http://VMware.Vim.VirtualDevice|http://VMware.Vim.VirtualDevice]$dev
	$temp.device.connectable.connected = $false
	$temp.device.connectable.StartConnected = $false
	$temp.operation = "edit"
	$spec.deviceChange += $temp
  }
}
$vm.ReconfigVM_Task($spec)

This changes all serial ports to "disconnected" and will also unselect "Connect at power on".