That is your heat riser. All that does is provide a small amount of warm air from the exhaust manifold into your intake to keep the injectors and throttle plate from getting frosty during the winter. If you go with an aftermarket airbox, just remove the heat riser and cap off the vacuum line going to the stock air box (that vacuum line controls a "blend door" inside the airbox to vary the amount of warm air going in to the intake).
Yes, the flexible tube can be removed. You won't have to put anything over where it attaches to the manfold because all that piece of metal is is a holder for the tube. Air won't blow out of it or anything.
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