Sure it can be locked. Depends what you want. I'm assuming you want to make it incompatible with Hyrule Magic, which means incompatible for changes with this program (like Parallel Worlds), which is done in hex. Experienced people however, can still reverse the lock in hex, or make any change in hex directly. And can still make a repro-cart out of it.
Second option is to change the format from lorom to Exlorom and make some more additional hex edits of course. This also protects from gfx extraction (as well as any editing), but only a small amount of emulators will support this format, specially if you choose it to be 8MB, instead of 6MB expansion.
Third option is to prevent making phisical carts (since we know many repro cart makers are making huge money with Z3 hacks owned by Nintendo and the modders).
But of course this is a double-edged sword, since more "locking" means lower compatibility.