I'm not thinking it would really be a huge problem off road. Maybe if you get into a deep water crossing that is over the cutout, but at that point your stock exit point would also be submerged. While the truck is running I think there's plenty of pressure to keep anything nasty from migrating forward to the engine.
I wheeled my old GMC pretty extensively and I had it straight piped and dumped right under the bed. I never had a single issue with it even during water crossings and in mud holes. So as for myself, I'm not worried about it a bit off-road.
Edit: Realized you might be talking about the moving parts getting gummed up. As far as that goes, I'm hoping the electronics are sealed up, if not, I'll be doing that. Hopefully the rest of it is designed to handle dirt and debris as well. The HPE cutout comes with a 5 year warranty, so at worst you'd have to test that out.