I doubt there are any private locked parking facilities in Holyhead, apart from those belonging to hotels/b&bs such as ferrylodge.co.uk/carpark.htm...
However, the long-term parking for the ferry service is patrolled and has CCTV coverage. There is a shuttle bus from the car park to the port terminal. Parking costs 5GBP per day/20GBP per week.
I do not feel you have any real cause for concern about the safety of your vehicle in the ferry car park.
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