Hi Nick, the vacuum gauge is intended to show a restriction in the filter media. It would also measure any restrictions back to the tank. If the day tank is the lowest point in the system, it should always be full, therefore there shouldn't be any siphon effect, perhaps what you are describing. The day tank should have a float mechanism to shut off the fuel when the tank is full otherwise it might overflow. If it's shut off, no vacuum.
If the fuel tank has its outlet at the bottom and your shutoff valves are leaking in air, you have a restriction in the tank, probably a screen that's blocked. With the head pressure of a tank, it should flow very well. If it flows uphill such that it needs a pump, the vacuum should be negligible unless there is a restriction. Once the pump stops, so should the vacuum. Most of us just have an engine driven pump, ymmv. My conclusion is that if you are showing a vacuum with the engine stopped, you have an issue.
What am I missing?