Eyes put people off. Bones too I guess. And if you are squeamish about offal, then eating a whole fish will include all of that. So some people don’t like whitebait because it all goes down the same hole. The fact that said liver, bowels and eyes are so small in size to register does not seem to matter.
I (of course) like eating thinks whole, and all of animals. Admittedly small animals as the bones can tend to cause a problem, though a wodge of bread can help out on fish up to the size of a big sardine. As well as the whitebait I have eaten whole locusts, shrimps, snails (sans shell) and now I am happy to say whole freshwater crabs. With shell. 50p piece sized bodies, claws and carapace make them pretty crunchy, but nicely spiced and very moreish, with plenty of nice meat inside. I ate them at Highway 4 in Hanoi, though they are not unusual on Vietnamese menus. And I recommend, if you like eating things whole.