From this conversation on GitHub it seems that there will be a choice.
In general we're moving away from runtime minification and are trying
to follow what the current client side ecosystem is trending towards,
grunt/gulp/bower etc. When we play in that world we get the benefits
of the ecosystem for free without having to rebuild all of the
extensibility ourselves.
That said, it is a choice thing and we'll be pushing people down that
path, but libraries like SquishIt will always be around and will
likely support ASP.NET as well as ASP.NET vnext.
So, in summary Microsoft are pushing people in the Grunt (etc.) direction, and it will be the preferred route, but not the only route. It won't "replace [the StyleBundle/ScriptBundle] mechanism" but give you additional choice. However, it does seem (reading between the lines) that StyleBundle/ScriptBundle may not be (as) actively developed any more - as they are Microsoft technologies. But if you want the same kind of functionality then it make make sense to move to a framework like SquishIt.