As far as I understand, there are plugs which get inserted into holes in the drain once they are ready to fill. This is to give the groundwater a place to go (into your pool) instead of popping your pool out of the ground. I was more concerned of water, especially dirty water, staining the plaster. But, I'd assume the acid wash would take care of any staining that may happen overnight.
Those plugs you refer to are/were in the gunite and are filled right before they do the plaster. Those holes you see are the actual drains that should be connected to your pool plumbing leading back to your pump filter, just like your skimmer. You should be worried about staining, leaking pipes, etc.
We did a re-plaster in July. Exact same thing - hydrostatic values and dirty ground water. I was so worried. However, after the acid wash no issues and you can not see anything to indicate staining. It was normal for us.