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I used to have a 1990 Plymouth Laser/Mits Eclipse. I had a sun roof put in and had a little deflector for it. Without the deflector and the sun roof open, my car was an enormous coke bottle, there was this loud low pitch vibration from having the sunroof open. I don't expect the deflector of yours was preventing this.
The reason for your deflector I'd imagine was not for debris management, but rather it helped create a low pressure area so when you opened your sunroof a few inches, it would really draw a huge amount of air out of your car increasing circulation. And it probably helped with wind noise as well.
I think you're better off not having the deflector, and your "non-smooth surface" concerns are unwarranted. Significant flow separation requires more drastic obstacles than what the little bumps on your sunroof present....don't worry about it.
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