It's the same way with the penny.

Tax on a 0.99 item isn't coming out to an exact penny multiple.

So stores are already dealing with this situation

Yes, stores are dealing with this alongside a whole legal framework today. They would not have the benefit of that for any changes without pennies, and in a few cases may open themselves to legal liability by underpaying state sales tax, overcharging snap recipients, etc etc. We don’t know because this was just a tweet decree by the executive while the legislature has been paralyzed.