Nope, masterpages are essentially dead. You can stay in "classic UI" and keep using them for the time being.
They have no guidence for how we can do any level of branding in modern UI. Other things they are killing include usercustomactions (which is what we transitioned to to get away from master pages). One of our critical customizations is a global enterprise navigation injected into all site collections and all sites.
Much much much angst and conversation about this in Yammer.
Supposedly new stuff coming down the pipe, but no clue what it will look like.
I would also say that eve in classic view it's not a good idea to use a custom master page...you could do it, but you were also responsible to update your custom masterpage with any new stuff added by Microsoft to default masterpages