I’d say this is a bug. Invoice that comes to total of zero should be introduced into cash-basis general ledger right away. However, for your type of business you should not be using Sales Invoices tab at all. You don’t have debtors.
Instead of sales invoices, you should use Inventory Write-off tab. When you do stocktake, figure out how much inventory is “missing” (either due to sales, theft or damage) and write it off to your Sales account. That’s it.
Yeah, this is still unsolved problem. Mostly because it’s not really invoice which made entry into general ledger, it’s transaction which paid for the invoice. I do want to improve the clickability on cash-basis but don’t have good solution yet.
I’d say that’s correct. If you are paying taxes on cash-basis, you probably don’t care about financial statements on accrual-basis.
Do not give your accountant any reports until your figures are correct. I will be looking into this issue of zero-total invoices on cash-basis. This would be a bug.