Not a lawyer, but as far as I know this is another example of Trump highlighting shortcomings of current law. I believe you’re right that an EO can’t officially (re)name something like Lake Ontario (or the Gulf of Mexico, or Department of Defense). That said, Google, Apple, and Waze can choose to follow the order even though Congress has not passed any legislation addressing the name change either way (and this Congress likely just won’t). Similarly, official DOD correspondence now carries the “Dept. of War” letterhead, even though the name change was never made official by Congress.

TL;DR: The people who are supposed to enforce the laws and the ones supposed to be making them are being very selective on which laws mean anything.