Yeah, after some research it appears to be somewhat common amongst Mojave users, but I have two friends also using Mojave who had never heard of it. Decent explanation of it in this comment https://music.stackexchange.com/a/79410
There were two basic workarounds: Launching Audio/MIDI Setup's MIDI Studio window, which force-initializes CoreMIDI;
this has to be done before launch every time. Apparently, there was also some known conflict with Korg drivers, because running Korg's USB-MIDI Uninstall utility https://www.korg.com/us/support/download/driver/1/285/3856/ solves the problem as well -- though for me, that simply means the Error dialogue doesn't launch every time.
Unfortunately, besides those two things, everyone's solution was simply to upgrade to Catalina, which I can't do on this machine.
No issues with my cables, have tried several ports, don't use any hubs. I'm coming up with nothing, which is why I'm fairly certain the issue still lies with that CoreMIDI issue.