That recipe is ambiguous, for just the reason you cite. The "most correct" (which is an oxymoron!) would be:
C. Add 100 ml of ACN + 1 mL of acetic acid + 899 mL/water.
However, with mobile phase prep, correctness is less critical than consistency. Hopefully the original method references an explicit procedure that was used to prep the mobile phase.
Agree with Tom, precise un-ambiguous instructions are the desired target, but each writer knows what "he" intends, but may be confusing to a new reader. In my first publication, a reviewer asked if my filtration was by vacuum or by gravity, and of course since I had done the procedure myself so many times, I "knew" what I intended, but was not clear to reviewer.
I like "C" as well, as any mix done by an HPLC pump is by volumes of each stream.
Even more confusing can be when mobile phases containing organics are taken to a pH. I prefer adding modifier (like acid) by volume or weight, more reproducible in my thinking.