My engine cover blocks a lot of dust and dirt from settling on the engine top, which I appreciate when I go pull the spark plugs.
Unless you're really hard up for cash, might be worth holding on to it and any other little pieces you may remove. When we buy these cars, we think we'll own them forever, but a lot of genvibers end up selling their Vibes, and the absence of things like the engine cover make the car look harder used.
Some people here have dressed up their engine bay by painting the engine cover.