As you've already mentioned, the game will fail to render the quantity to a human-readable number of the current value.
Referring to the Emerald disassembly, the items are stored as u16 Item, u16 Quantity.
https://github.com/pret/pokeemerald/blob/9952b676db9d2c8d5e71f7339eb000d8aa496ab4/include/global.h#L582-L586
So, the quantity can be at most 65535 (2^16 - 1). PKHaX already lets you set whatever quantity you want (that can be stored by the structure, aka 65535 max in Gen3). Any issues? Try it and see.