I always thought that the protagonists within the franchise had it mostly easy when encountering new species, save for the occasional Borg (well, when they first appeared anyway), the Viidians and "The Clown" (from the VOY episode "The Thaw"). I would think that as vast as the galaxy is, there would be a lot more exploration vessels presumed "lost" during their 5-Year Mission tour, due to unfortunate encounters with unknown alien species...