Ok, I know that one guy back in v20 found an obscure fix that allowed him to see emitters through water, but I don't know if it's applicable.
I was one of the people who pestered Badspot about fixing these in the Bugs topic in the dev thread. He insulted me in response and called it "lowest possible priority".
I still wish it were fixed too, it breaks one of my gamemodes that I was working on pre-v21, but I somehow doubt it'll ever happen. After all, every new revision introduces new content filled with new bugs that need fixing, and since new content is higher priority than fixing transparency, it will remain forever-low-priority. That's my guess.