"See I know the simh emulator does scan the USB ports for disk images and I wondered if that might cause issues."
You should be able to set it up in a way that won't cause any issues. First, the PiDP-8/I doesn't even scan the USB media unless you explicitly use the SingStep switch. Second, on scanning, it is only looking for a limited set of file extensions:
*.pt for paper tape images
*.dt for DecTape images
*.rx for RX01/RX02 floppy disk images
*.rk (or, *.rk05) for RK05 hard disk images
and maybe *.rl for RL01/RL02 images
Just don't have any files with these extensions in the top-level directory on your boot drive and you should be fine. The PiDP/8/I scans all mounted USB media, so putting your simulated images on a separate thumb drive will still make them findable.
-- steve