That's a terrible downside for servers. Flowing blocks are a real PITA for servers.
You'll only ever have flowing water if you run into a cave or something. It places a source block every time it mines a block, so once it's done, it won't cause any more lag than an ocean.
The real downside is that it's a lot more complicated to set up than a quarry (especially if you're using slickwater), and can't mine out as large an area at once. The max is an 8 or 9 block radius if I remember correctly.