I think you'll find the reason for the apparently heavier security scrutiny is because they have targets to meet for e.g. numbers of shoes taken off, numbers of mobile phones "sniffed" etc. When there are only very few flights, more of the pax are subject to these 'random' extra checks.
Caernarfon would require significant upgrade to support commercial air transport. It has no instrument approaches and RFF only Cat 1.
NS