The sense I got from reading the SC Ruling is that the Court was neither satisfied nor dissatisfied, per se, with the Minister's ruling, and merely were satisfied that (a) the decision was not unreasonable based on the information available to the Secretary of State at the time (Javid), and (b) the authority to make such a decision had been entrusted to the Secretary of State by Parliament. Therefore, it was deemed inappropriate for the Courts to step in and make the decision themselves on Begum's citizenship, or the dangers it may or may not pose to National Security; doing so would in principle run against the ideas of Parliamentary Supremacy and Separation of Powers.
For all that is often said against the legal system, for the most part, they understand -- as a collective, at least, if not always individually -- their role and the limitations of it. If Ministers trample over their own laws, or fail to understand the country's Constitution, it is their own fault when the Courts say so. On the other hand, any one judge or Court may be mistaken; this Judgement is as scathing as it's possible to be in a document like this about the Court of Appeal's previous decision in this case. It's also manifestly preferable for it to be *difficult* for a Minister to revoke anybody's citizenship, rather than easy.