I believe liquids are hardcoded. Otherwise we'd have rivers of booze and blood popping up in mods every now and then.
I confess to removing aquifers, and all non sand soil, If only so I can skip the painful process of site finding. Having an awesome idea for a megaproject ruined simply because you don't feel like spending another hour genning sites to find one that actually has sand as well as everything else you're looking for is dissapointing. And aquifers... aquifers simply aren't fun.
I'll agree you can't do your best megaprojects on aquifers but aquifers can be a bunch of fun, if you use the correct multi-aquifer drilling techniques you can smash through an unlimited amount of layers quickly, and you feel cool doing it. Also, some of my best memories come from aquifer related hijinx; once, I breached HFS and they were swarming the mines, killing dozens. One brave dwarf attempted to remove a wooden wall holding back the aquifer while the surviving champions fought to protect him. He finally removed it and a flood of water washed down into the mines, almost saving the fort forever (one had snuck by before oops).