I have a recently cycled 29g with black canopy, stand, painted background, and sand. I love the look of it even after I've had some detrius build up and algae growth. I haven't had any problems with it being magnetic, and I have a YWG / candy cane pistol shrimp combo that have an underground castle down there, so I don't think burrowing is a problem either.
Eventually, it comes down to the look of it, and what you're going for. Over time, rocks will erode and create more of a speckled look, so it will never be as jet black as when you first put it in. However, some have had luck syphoning out the top layer over time with water changes and adding fresh on top to preserve the look.
Bottom line, totally up to you, but if you go with the black look, do some research on here to get the kinds that aren't magnetic. I would recommend!