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I have not seen a pygmy seahorse myself, but believe that they (and other sea horses) ARE quite sensitive to the strobe flashes. I am not sure about killing them, but have seen comments that they will move away from their location...this opens them up to predation, lack of ready food source and other nasty things.
Prudence would dictate not shooting 250 images with strobe in a row of the same creature, but a couple of flashes here or there does not seem to cause much negative impact...if you check out some of the posts on digitaldiver.net there is a guy there who regularly finds the same ones and they get many photographers through each week.
They are certainly sensitive to light, but it certainly is not killing them (I took images of the same one several days in a row while in the Philippines).
The site I was at has two large sea fans which is the home of many of these - I counted 10 on one and 15 on the other. People photograph them regularly - probably they see a photographer/videographer every other day.
As long as you (and everyone else) is not going overboard, it isn't going to kill it.
I hope not. At Lembeh Strait, there are a few well known seafan with local resident pgymy seahorses at the pier which have been photographed by just about every diver with camera for a number of years. If strobe kill them, I doubt that there would be any pgymy seahorse left in Lembeh.
It seems unlikely, but who I am to make a definitive judgement. One thing you do have to be careful about is that if you light them up (e.g with a focusing light) long nose hawkfish may quickly dart in and eat them.