We are an Educational institute and have many sub-sites for each subject and
we will have different elements on each sub-site quick Launch bar.

We are thinking we won't be able to do a global change on the Top navigation
if we have multiple master pages for each subject matter.

Is this a better approach to call Quick Launch bar from different page
layouts? If we go that route what are repercussions of doing that?

Also we are not going to have left Navigation and different look on the home
page, so do we need two master pages one for home and one for rest of the
site.