So is clinical significance determined in part by perceived significance? I feel that a potential 2% risk of conditions as serious as those mentioned in the article could easily influence some people towards choosing to have kids at a younger age.
It's determined entirely by perceived significance. For each type of drug, there is usually some agreed on metric within the field that determines what constitutes clinical significance. E.g. a blood pressure drug might have to lower blood pressure by 5% or 10% or whatever. And often times the metric isn't even relevant, as in the case of a reduction in blood pressure vs. a reduction in total mortality / morbidity.
However, at the end of the day what the academic community considers clinically significant doesn't really matter, it's your own preferences and values that should be your guide. Especially since in practice everyone is basically out to trick you in order to make more money, from pharma companies to newspapers to academic journals to professional organizations (AMA, APA, etc.), etc. That's why it's important to really understand this stuff forwards and backwards and to keep your wits about you.