Yes, I will be getting a vaginectomy.  I cannot stand the thought of having a hole there.  Of all the things to be dysphoric about...
In researching metoidioplasty, it seems that a number of surgeons actually leave the vaginal canal intact.  They therefore must leave a small hole in the scrotum (some don't join the scrotum at all) so that any fluids from said hole can drain.  Apparently there still are fluids even if a hysterectomy has been performed.  Yuk.  
There are, however, some surgeons who will remove the hole.  From what I understand, Dr. Miroslav Djordjevic totally removes the vaginal canal and then extends the urethra through the neo-phallus when he does metas; a hysterectomy is required.  Also, there are cases when females (who are happy to remain as such) must have the vaginal canal totally removed--usually due to cancer.  So it is entirely possible to 'close the hole,' as long as a hysterectomy is also performed.  I see no reason why keeping the vaginal canal is necessary to prevent infection.