Black solder mask, along with a pour of epoxy around the critical parts, after cleaning, will do more than just removing numbers. At least the black will make reverse engineering harder, especially on a multilayer board, with tracks routed in the inner layers, and a less than visible amount on top and bottom, and the epoxy pour will keep them from moisture.
All that will mean the cloner will just have to sit there and do extra steps to get a full circuit design out, so best, if you are using programmable parts, is to make sure to set the lock bits on them, and make it harder to just copy, plus if you can add an extra encryption to the firmware updates, so they are unique to each serial number, making it harder to simply reverse engineer an update to get the firmware. 10k units per year doable with only a few extra gray hairs a month. And yes for 10k units most suppliers of non jellybean chips will happily give you a custom part number for you to use in house, though you might be doing a bulk buy for a 3 year supply initially. Will just have a manufacturer mark and lot number on them, in addition to your custom part number. Otherwise invest in some paintable epoxy and do your own blacktopping of the parts after assembly, which is what the epoxy will be doing.