I only run a lower resolution if I have a good reason to.
One camera in particular is an old ACTi E77 which has a 10 megapixel sensor. It sounds good but really it isn't because the sensor and image processing are shit. So I run it at 3 megapixels because that yields basically the same level of detail but with lower CPU usage in
Blue Iris, and the picture has fewer compression artifacts.
I'm also still running several Hikvision 3MP cams at 2MP because the 2MP mode actually offers a wider (but also shorter) field of view than the 3MP mode, and I feel like the wider field of view is more useful outdoors. I run them this way even though the 3 MP mode actually has slightly better pixel density.
However for other cameras like my Dahua starlights and 4K cameras, absolutely I run them at native resolution.