Is there a shortlist somewhere that shows which of the animal photograph opportunities I'll only get one chance at? Bosses, areas I can only visit once, etc?

None actually come to mind. Almost all of them are either in an area that can be revisited, appear later in another area, or the photo is required to progress. If you miss photographing the first boss, for instance, you can photograph its skeleton washed up on the beach later. (There are more of those same bosses again later, too, but it's tricky to get a good pic while they're shooting at you.) Of course it's possible to miss a few if you aren't using a walkthrough, but I don't know of any that are COMPLETELY missable. The final prize is just a mdisk with all your pictures on it, so as long as you pay attention you should be able to get all of the pearls without using a walkthrough.

bevinator pretty much sums it up, but just a quick tip:
Remember it's not just about animals, NPC's count too, and some are unique in their species. For example your buddy Pey'j is the only talking pig around, and there's a cat lady you meet a bit later in the game who's also unique, same goes for the bull barman in the Akuda Bar. You might want to take pictures of them as soon as you can.

If you want to be certain you never miss one, just buy the animal detector from Ming Tzu and they will show up on your mini-map (only the ones you haven't photographed yet). He's a humanoid walrus and have a shop in the city (in the area that is closed in the beginning). He also sells other useful items, such as PA1s and a pearl detector.

They are not so hard to spot without a detector, though. First time I played this game I somehow missed Ming Tzu's shop (even though NPCs often mention it) and still managed to catch almost all of them. By the time I bought the detector later on, I only needed 2-3 photos.

This is the first boss that was mentioned. When you destroy that boss, you will notice the head doesn't disintegrate. Later, if you head to the left of Black Isle (facing away from town), you will find the head washed up in a cave and you can take a picture of it.

I remember missing one single photo on my first walkthrough and I just coulnd't recount where I could've missed one creature. It turned out to be the whale in space.
Had to play the whole game over again just to find out that you just get that lousy photo disk in the end...