i'm sure it would affect the fit of the bearing/threads to some extent, but you can always mask anything that you don't want anodized/bb. also, as long as the bb isn't too agressive you should be fine with the way the string comes off the top. i don't know if i'd bb it though. i'm sure it would look nice but wouldn't enhance the performance of the top...it might even increase drag and reduce spin times. but then again, if all you are looking for is aesthetics then go for it.
keep in mind that i am not speaking from experience in anodizing tops but yo-yos. i haven't done it myself but i am familiar with the process. the concept is the same. bb or ano on a yo-yo is great for tricks, but like i said above, you would probably only improve the look of the QS. btw, you aren't going to try anodizing at home are you? i'm assuming you will be going to a professional.