The rapid integration of generative AI into academic writing has prompted widespread policy responses from journals and publishers. However, the effectiveness of these policies remains unclear. Here, we analyze 5,114 journals and over 5.2 million papers to evaluate the real-world impact of AI usage guidelines. We show that despite 70% of journals adopting AI policies (primarily requiring disclosure), researchers' use of AI writing tools has increased dramatically across disciplines, with no significant difference between journals with or without policies. Non-English-speaking countries, physical sciences, and high-OA journals exhibit the highest growth rates. Crucially, full-text analysis on 164k scientific publications reveals a striking transparency gap: Of the 75k papers published since 2023, only 76 (~0.1%) explicitly disclosed AI use. Our findings suggest that current policies have largely failed to promote transparency or restrain AI adoption. We urge a re-evaluation of ethical frameworks to foster responsible AI integration in science.