LLM-based Search Engines (LLM-SEs) introduces a new paradigm for information seeking. Unlike Traditional Search Engines (TSEs) (e.g., Google), these systems summarize results, often providing limited citation transparency. The implications of this shift remain largely unexplored, yet raises key questions regarding trust and transparency. In this paper, we present a large-scale empirical study of LLM-SEs, analyzing 55,936 queries and the corresponding search results across six LLM-SEs and two TSEs. We confirm that LLM-SEs cites domain resources with greater diversity than TSEs. Indeed, 37% of domains are unique to LLM-SEs. However, certain risks still persist: LLM-SEs do not outperform TSEs in credibility, political neutrality and safety metrics. Finally, to understand the selection criteria of LLM-SEs, we perform a feature-based analysis to identify key factors influencing source choice. Our findings provide actionable insights for end users, website owners, and developers.