Glowing water absolutely works in a deployer to kill mobs for minium shards. The only other thing I've tested is a lightning wand I had lying around (didn't work), but I'm guessing a fire wand or any other right click weapon that damages an area should work. It's not really a bug with the deployer, given that it IS doing exactly what it says it is supposed to do, but it is a workaround of the intended mechanic of the minium shard. To fix it, they deployer would either need special exceptions (perhaps a list of IDs in a config) for certain items or other mod authors would need to make sure area effect damage is not linked to right click if they don't want it used in this fashion. While railgun automation is relatively easy, glowing water minium requires automated gathering of other resources and careful timing to avoid lagging up the server. That being said, I'm just short some demonic bees for the glowstone.
Here's what you need for automated glowing water farm (even without the deployer-minium thing, it's a fun item and used for making holy hand grenades):
Lots of sand. I've been quarrying in desert biomes anyway, so it's mostly a non-issue as there are lots of ways to get tons of sand.
Auto smelting of sand to glass and auto crafting of glass to glass panes and auto crafting of glass panes to empty vials.
A deployer on a timer filling empty vials to make vials of ordinary water.
A netherwart farm. I used golems and had them dump stuff into an ender chest connected to my me network.
A gunpowder farm. Tier 5 creeper shard or lots of Austere bees.
A glowstone farm. Demonic Bees, a witch farm, or a complicated setup using the tome of the alkahest, a redstone farm, and an initial glowstone dust to turn redstone into glowstone.
And there you go!
Throw a zombie pigman farm on top of this for golden nuggets for making holy hand grenades (you'd already have all the stuff needed for a tnt farm at this point as well).
Also, if in thinking of building your house out of Holy Planks of Sengir (because why not), don't. They're just oak planks if you place them.