Free is not the deciding factor
Both products have a genuinely free tier, so price is not what separates them. What separates them is scope. An invoicing tool assumes the transaction is a bill: you did work, you charge for it, you get paid. A shop transaction is five things happening at once — stock moves, credit goes onto an account, material may leave on a truck, cash enters a drawer, and GST accrues at the item's own rate.
Where a shop feels the gap first
Usually stock. A business that bills without moving stock has an item list rather than an inventory, and within a month the figures stop meaning anything and ordering goes back to walking into the godown. The second gap is credit: not a record of who owes what, but ageing, limits that warn before material leaves, and payments allocated to specific bills. Those decide whether the money comes back.
Units are the third gap
Service invoicing has no reason to handle an item bought in tons and sold in kilos, or tiles bought in boxes and quoted by the square foot. In a material shop that conversion is on most bills. Holding the unit on the item is what removes the arithmetic from the counter, and it is not something an invoicing product is built to do.
Where you should stay with Zoho Invoice
If you bill for work rather than goods, carry no stock and make no deliveries, an invoicing tool fits better and will be quicker to set up. Freelancers, consultants, agencies and most service businesses are in that position. We would rather say so than have you move to shop software and leave two-thirds of it unused.