Whales would be visible, along with all the life chemicals, so the analogy isnt that great.

I've flown in planes a handful of times, looked down at the ocean on plenty of opportunities, and never observed any whales. I'd say the analogy is perfectly great.

If the water was as transparent as space, whales and large schools of fish would certainly be apparent.

Space isn't quite transparent, and a closer analogy would be to ask if you can spot bacteria and other microorganisms because something sentient the size of a whale "scaled up to space" would be unrecognizable as such to us.

> Space isn't quite transparent

On Earth scale it is for all practical purposes.

Space whales!

A rather apt analogy, because you can see countless signs of non-equilibrium behavior, chemicals, heat, and other things (you really have never seen any, say, birds while flying?) that tells you you are not on a planet devoid of life.