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.
The situation where pennies exist already has all the problems concerning rounding after sales tax. Things are rounded to whole pennies. The same solutions can be applied to round things to whole nickels.
Tax on a 0.99 item isn't coming out to an exact penny multiple.
So stores are already dealing with this situation