That is an interesting point, if I was to make a guess I would say it's a management decision made many years ago that it's just easier for the arms regime management - to simply consider all firearms licence holders as 'in possession' of arms items requiring secure storage as per the act and assessing security as such at the time of vetting (a money and labour saving decision, not a 'compliance' one).
The way that is worded, would appear to align with what you are suggesting in that not every firearms licence holder needs compliant security if they currently aren't in possession of arms items. The security requirements only kick in if the licence holder takes possession of arms items.
Interesting point.
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