Regarding the SAI, nubcake can definitely code around it to make it pass the readiness test, even with all the hardware removed. We did that on my car. The visual test is the real problem. Removing and replacing the pump is easy, so it would certainly be possible to temporarily reinstall it for a visual test. The plumbing behind the heads is much harder to remove/replace with the engine installed, so if the visual test was thorough enough to check that, it would be a problem.

If you choose to leave the system intact, then there is no point in coding it out, it doesn't do anything that affects performance.