Using the proleptic Gregorian calendar for historical dates is only a problem if you want to compute the day of the week (which those missing days will throw off prior to the adoption of the Gregorian calendar in the relevant country) or the number of days between two historical dates (if the two dates span the date when the Gregorian calendar was adopted).

And, frankly, there are other problems to deal with beyond correctly handling the Julian/Gregorian switch. In Nelson's Navy, for example, the new day started at noon rather than midnight as we'd expect. AM could be June 1st, PM could be June 2nd, and both could be Tuesday.

And then there are lots of historical events with dates like "on or about August 6th" or "mid-September" or the "in the Fall of".

Trying to deal with historical dates in what a programmer would consider a perfectly correct way is something of a fool's game.