Gadzooks. Hard to believe I actually used to teach this stuff. Organic nomenclature is far easier, there's a set of rules at least. In the basic molecules, like water, ethanol, peroxide, etc., they existed far before any rules were introduced.
H2O is written that way because it's the empirical formula. During exercises where structure is important to the chemical reaction, it was always written H/O\H (it's supposed to be a triangular shape). When doing chemistry on paper, sometimes the three-dimensional shape matters, sometimes it doesn't. I recall doing plenty of things where I had to write out H2SO4 in it's actual shape with charges and all that. In reactions, the shape is important much of the time.