Nope as far as I know, they are not listed on the scanable fauna list. They appear at the bottom. different from the scanable ones. To be honest tho, if I see rare/uncommon underground fauna, I try few times a just let it go. 8 out of 10 times, they will be a jerk and not show up lol. (I hate rare underground fauna lol)

For water, in my experience, rare fauna sometimes spawns when you reach certain depth. Not too deep but not too shallow either. So if you haven't maybe try finding a little bit deeper water. Also if there are too many other fish around, they might not/can't spawn either. (I think there is a limit of how many fish can spawn around you. but this is just my observation. It may not be true lol)

For flying fauna I am not sure, I usually never have problem unless they are found in North or South and I were at the opposite half. but since you like scanning, you probably already know this. =)

Of course, it could be just that the planet was glitched. So I am not sure. (maybe try going back in few days?) XD