It's likely that what they have done here is access the fuse box by cutting a hole, not with a view to stealing the van so much as getting into it to steal its contents. They will have bridged a relay to trigger the central locking, which will have allowed them access to the van. Short of repairing the hole, there isn't really a lot you can do other than fit secondary door locks or separate alarms that aren't wired into the van's ECU.