Don't worry, you won't scratch your screen. The buttons are placed in a way that you can easily access them with your thumbs. Pulling the stylus out all the time would be very unpleasant and awkward.
I don't think Ol' Ninty will force any mic thingies, but they've done it before, so I wouldn't be surprised if it was that way.
Either way, it doesn't bother me at all to use the mic.
Iwata already confirmed that OoT 3D will be crammed with content not in the N64 version (http://3ds.nintendolife.com/news/2011/03/iwata_ocarina_of_time_3d_crammed_with_new_content), and we've known a long time already that Ura-Zelda was finished but never released...