First, I think it is a very bad habit of servers who do not inform their guests whether things they offer are an additional fee.
We were lucky that our servers always informed us. I know that on our latest Palo brunch our amazing server Pamela offered us coffee and clearly stated that the regular coffee was included, but that they had a selection of espresso drinks which would be an extra charge. The same with water at Remy.
I would actually let it be reflected in my tip if a server tricked me into ordering something that I would not have paid for had I known it costs extra. However, when I am not certain about something I just ask if what they offer is included in the experience or an extra charge.
And finally on the sparkling water situation: all
DCL cruise ships serve soda water (or however you want to call it, club soda or yes, in some areas of the world: sparkling water) for free in the MDR. It is my drink of choice and I never paid for it. It comes from their fountain, not from a bottle. So, I don't think it is crazy to think it would be included at Palo and Remy as well. The other sodas are (my BF had Coke for every single meal we had in those restaurants together, we were never charged).
OP, to come back to your question, what additional charges you need to be aware of, besides bottled water and speciality coffee I think the only other things would be upgrades to the meal experience like the wine tasting menu for dinner. However, this was marked clearly in the menu. But if in doubt, just feel free to ask. I don't think asking implies that you cannot afford it, only that you want to make an informed opinion.