In the era of pervasive cyber threats and exponential growth in digital services, the inadequacy of single-factor authentication has become increasingly evident. Multi-Factor Authentication (MFA), which combines knowledge-based factors (passwords, PINs), possession-based factors (smart cards, tokens), and inherence-based factors (biometric traits), has emerged as a robust defense mechanism. Recent breakthroughs in deep learning have transformed the capabilities of biometric systems, enabling higher accuracy, resilience to spoofing, and seamless integration with hardware-based solutions. At the same time, smart card technologies have evolved to include on-chip biometric verification, cryptographic processing, and secure storage, thereby enabling compact and secure multi-factor devices. This survey presents a comprehensive synthesis of recent work (2019-2025) at the intersection of deep learning, biometrics, and smart card technologies for MFA. We analyze biometric modalities (face, fingerprint, iris, voice), review hardware-based approaches (smart cards, NFC, TPMs, secure enclaves), and highlight integration strategies for real-world applications such as digital banking, healthcare IoT, and critical infrastructure. Furthermore, we discuss the major challenges that remain open, including usability-security tradeoffs, adversarial attacks on deep learning models, privacy concerns surrounding biometric data, and the need for standardization in MFA deployment. By consolidating current advancements, limitations, and research opportunities, this survey provides a roadmap for designing secure, scalable, and user-friendly authentication frameworks.