Having kept reef fish for many years I'm yet so see any react badly to a flash being triggered, but I can imagine that if it was mere inches away they might get a bit narked! The vast majority of their senses are in their "latteral line" which runs along the body. This senses vibration and electric fields etc so light is not such an issue to them.
I normally shoot with the flash on a tripod at 45 degrees to the glass, leaving me to move around freely. You won't be able to in this instance but try to block out as many background reflections as you can.
You MUST keep the lens perpendicular to the glass or the refractive index difference of the air/glass/salt water will bend the light beyond acceptable limits. In short, it'll look awful!
Here are a few I took of a friends 17,000 litre "tank" a few months back.
A scribbled Anthia (wreck fish):
A Clown Wrass:
And a rare Tang cross breed:
Interestingly, the guy in question has actually helped Blue Planet to rehabilitate fash that they've had passed on to them from the public. He actually had a baby Hammer Head shark in his stock tanks for a while which they couldn't get to feed. Someone had imported/purchased it as a purse and once it hatch realised what they'd done! It was amazing to watch it gliding around his tank harrasing the other fish in there and yet it was SOOO small, almost cute!