Get your taxes done using TurboTax

Well...I don't disagree with you in a strict form-filling sense..

BUT...we are dealing with software calculations here....(and only talking about actual distributions and not rollovers)

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The NY state forms "start" with (close to) the Federal AGI in lines 1-19a of the IT-201, which includes the box 2a amount of a 1099-R  (if a real number) or the Federally-taxable amount of box 1 if box 2a is empty. 

Then, for people in one of the  NYState or City retirement systems, those amounts are subtracted from NY income, down in line 26 of the IT-201......but..... the software uses the NY distribution amount entry to "subtract" that distribution amount, so if you leave the NY distribution as  blank, or zero, then nothing is subtracted from NY income and all of it is included.  That the software ends up putting that in box 16 is immaterial...since it isn't usually used for anything else.

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Then if the 1099-R is not from the NYGovt/City systems, nor a Military 1099-R, which is the case for 94.965% of all 1099-R forms issued to NY residents, a Pension deduction is allowed up-to-$20,000 on line 29 of the IT-201........now, I haven't checked to se what the software uses, but I suspect it also uses the NY distribution amount too...so if the NY distribution amount is left a zero/blank, then there is no deduction.

Why doesn't the tax software just use the 2a value (or Federally taxable amount of box 1 if 2a empty) instead and ignore box 16 altogether....don't know...there are a billion ifs-ands-buts-exceptions where the calculations may not go right if that is used.  (I think I saw a post earlier that some paper Maine Govt pension 1099-R forms have box 16 actually filled in with an entirely separate value for some special ME-calculations.)

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Do some issuers enter a zero in box 2a, when it should be left blank?   yes...that can happen.

The only cases I know of where box 2a can validly be a zero is for direct-transfer/rollovers to another retirement account of the same type (meaning Roth or not Roth)...perhaps occasionally for refunding of over contributions....(and some rare traditional 401k-to-Roth 401k or Roth IRA transfers where only after-tax contributions are allowed.)    BUT...Someone may think of some other situations.