If I take off the spoiler on my 89 GTU, will it leave ugly holes lining the back of the car? How would I get rid of these?

 

You could get plastic caps from a parts store (like the ones used for interior trim) or have a welder weld in some metal plates and repaint. Just put a rubber S4 sport spoiler on there

 

If your spoiler is in good shape I would love to buy it from you. PM me if interested. I would suggest having the holes welded, but then you would need to respray that area or it will look weird. You could use rubber plugs but they would also look weird, but they would keep the water out. Those are really your only choices.