There was an interesting exchange on one of the cryptozoology lists about whether there are surviving prehistoric whales (Basilosuarus sp.) and/or other large, spectacular marine animals still undiscovered. A summary of my inputs on this:
I do believe there is at least one, and maybe two, species of large marine animal behind the hard-to-explain "sea serpent" reports. The one I am quite certain of is a huge eel or eel-shaped fish. The less certain one is a long-necked type that is most likely a large unknown seal or sea lion. I think the usual factors of mistake, exaggeration, etc., combined with sexual and perhaps geographic differences, in these two species would account for enough of the more convincing "sea serpent" reports so as to explain the whole business.
I don't agree with those scientists, eminent though they are, who consign said "whole business" to legend. There are just too many impressive reports by ship's officers and other witnesses who, if they were not marine biologists (and remember that Messrs. Nicoll and Meade-Waldo, famous for a clear sighting in 1905, were in fact well-qualified biologists), could still be relied on to know a whale from a giant elongated "something." We know from well-qualified observers there are at least two species of beaked whales for which we have no specimen and no scientific name. The ocean is still a big place.
There are cryptozoologists, some more qualified scientifically than I am, who argue that several animals are evidenced by the sighting reports. I have difficulty, though, with the idea that a plesiosaur, a long-necked pinniped, a basilosaur, a giant crocodile and a mosasaur are still out there. The body of sea-serpent reports convinces me at least one animal must be undiscovered, but does not convince me that several types of such animals remain unknown to science. Not with no unquestionable bodies found, no post-Mesozoic fossil records verifiable, no specimens having swum into fishing nets, none ever being harpooned (and only a couple even spotted) by whalers, etc. (Allegedly lost, misidentified, or "suppressed" evidence is not worth anything as evidence, because it doesn't matter why we don't have it. All that matters is that we do or do not have it. And a report of a carcass found and lost is no stronger or weaker evidence than an individual sighting report. It is a sighting report, it's just of a dead animal.)
(As an aside, it's actually a bit odd how the vertebrate world seems to have almost given up on long necks. A few mammals, a few turtles, no other reptiles, no amphibians. Only the dinosaurian-derived birds seem to put much stock in long necks anymore.)
Science follows (or should follow) where the evidence leads, without preconceptions. The question is how strong the evidence is, and, unless you've got a carcass in your office, there's no avoiding some degree of subjective judgment on that. The probability of discovery does factor into that judgment. If we had, for example, several seemingly good accounts of 21st century mammoths in North America, I'd still discount them, because the chance of the animals remaining hidden until now is so close to zero. The chance that science has missed every one of several breeding populations of large bipedal primates on four continents (N America, S America, Europe, and Australia) (and on most of Asia), a position held seriously by some experienced cryptozoologists, likewise seems to me very close to zero. I think we will find at least one (Sumatra's orang-pendek), and one or two others are at least possible. But not a whole zoo of them.
Since this is my blog, let me toss in my opinon about the recurring belief of some cryptozoologists that evidence once reported and now unavailable may have been "suppressed by science." I'm not saying that all evidence is viewed dispassionately and treated properly. Let's say a paleontologist finds a plesiosaur vertebra that appears only 20M years old, when the established wisdom is that all such animals died out 60M years ago. I could imagine her talking herself out of publishing about it because there's such a strongly established body of thinking behind the 60M year date. She may think "It must be my mistake" or "I'm not putting this out there unless I have a dozen more like it and three other paleontologists who have duplicated my dating results and will say so in print."
A scientist with a dead plesiosaur (or whatever form of "sea monster") in his museum is another thing. A recent carcass will hold up to any storm of criticism or ridicule while making the discoverer famous for all time. I'm quite firmly convinced that no dead sea monsters (or sasquatches or Homo erectus specimens or whatever) are stuffed in vaults because someone found them inconvenient.
All that said, there are still compelling zoological mysteries still to be solved. I hope we will solve them. I won't be disappointed, though, if there are some we never do. I think that's good for us.