I don't think I would confuse the two themes if I heard them - I think Saq covered it with his post.
I think it's an effect of the types of instruments and sounds used that conveys an aquatic 'feel' when listened to.
Although, I do think the SeaQuest theme has a hint of Star Trek in it near the start. Anyone else ever thought that?
'If the Apocalypse starts, beep me!' - Buffy Summers
'The sky's the limit.....' Jean-Luc Picard, 'All Good Things'
courtesy of Saquist