You are right, under the assumption of anonymity, that alternative does not work. Prints on file for a different reason, such as a prior conviction, would give

You are right, under the assumption of anonymity, that alternative does not work. Prints on file for a different reason, such as a prior conviction, would give you an ID. According to a link from the article, however, EncroChat was cracked last year. Stewart was presumably not one of those arrested at that time, which implies that either this crack did not yield enough information to ID him, or did not yield enough evidence to proceed against him. The former case could be solved if his prints were on file, and in the latter case, his prints might have led to additional evidence which had previously not been attributed to him. As the article says he was identified by his prints, the former seems much more likely.