If the factory had cutoff valves, there should be no issue with just shutting them off other than those valves can eventually start leaking. You definitely want to cap them off and not depend upon the valve to hold against pressure. You also want to secure the hoses so they can't flop around and get caught in anything moving, making sure they aren't bent into a kink and making sure that there is some ability for movement so the engine can't pull the hose loose under torque.
If I were doing this on my own vehicle, I would try to run a single hose from one port to the other at the engine, removing the hoses that the valves are attached to. If the hoses terminate into a screw-in fitting on the engine, I'd remove that fitting and screw in a plug. Every fitting and every rubber hose is a potential leak, and I would eliminate as many leak points as possible.
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