Indeed, not doing so can lead to errors that are damageable for civilians. We have to respect civilians, even if they are involved in big cases. So, i think the NYPD refuse to provide data on seizures because they are used to uncover abuses of the civil forfeiture process targeting low-income people.
The current computer systems for NYPD is apparently not able to handle the counting of large amounts of currency. The amount of unclaimed cash and property for NYPD was over $7 billion in 2015. A new computer system would help to record and audit the cash totals and prevent police corruption.
Law enforcement officers are people. They seize money for unfair reasons. They do not track it so that they can embezzle it. A computer system wouldn't help because the people using it would be no more honest with a computer system than without one. The only way to track the money is to have many people double checking the actions of others.
I do not think the fact that a 4-year old computer system would crash if queried for the amount of money the NYPD has seized as evidence is cause to upgrade or purchase a new system. That would probably be quite an expenditure in itself. Four years is not that old. If the present system cannot handle a simple query (and I really don't see a reason why it could not), keep a physical record. How hard is it to write down the amount of cash collected?