Fortunately this is not a situation I have to deal with, as my wife likes the audio system about as much as I do, and let's me spread out the equipment over about a third of the area of the entire family room, including thick cables out in the open, and the CD player and DAC/pre-amp on an end table next to my listening seat on the sofa. Of course, she's taken over the entire bonus room with her drum kits and piano, and has now taken one of the spare bedrooms to store accessories and drum cases. I do wonder where she thinks she's putting the vibraphone she wants so badly.
Anyway, Tim, the one right solution here is for you to explain to your wife that the subwoofer is an important and expensive piece of equipment, and a plant on top, fake or otherwise, is not going to hide the fact that it is a large, black, non-decorative cylinder. I would show up with flowers or her favorite token of affection and ask for her understanding in this situation. If that doesn't work, where she is so insensitive to your feelings, you have more problems than an ugly subwoofer, IMHO.
If the plant is fake, so there's no water involved, covering that port is unlikely to damage anything, but it may change the characteristics of the low frequency response of the sub, or it might make funny noises as air blows past the plant. Either way, this seems like a silly mitigation to the appearance problem.
