icecube: It's best for the positive terminal to be covered for safety. In the event that a piece of metal tool falls on the positive and negative terminal or on the positive terminal and metal body of your vehicle, Bzzzzzt lah! and your ECU may be fried.
A worst case scenario is if there is an accident and your hood cover folds, it may kena the positive terminal and Bzzzzzt again lah, unless you have a hood cover / heat shield under the hood cover.