That's something I didn't know.
Looking at vanilla BG2, you're dead right: there are 309 areas with a zero value of map offset, and no areas with a nonzero value but no map notes.
On BG2EE, on the other hand, there are only 40 areas with a zero value of map offset, 21 of which are OHxxxx areas. Conversely, there are 286 ARxxxx areas with zero features but valid offsets. At a guess, Cam or someone ran general patching code but forgot to tell Beamdog's own area designers! (I assume the other 2 areas in vanilla BG2 with zero map notes had some added in the EE.)
Since both conventions are present in game, and since the zero-value one is much less helpful, I agree that it would be good for CREATE to go with the valid-value convention. In general I 100% support your approach to backwards compatibility, but in this case, CREATE are is a sufficiently niche thing to do, and the scenario where bugs could be introduced is so baroque in any case, that you might as well just change it.
(Speaking of niche things to do, I worked up the WEIDU code to create a blank wed file, which CREATE can't do natively. You're welcome to it if you want it - though realistically the use case is so tiny that it might not be worth your time.)