I don't actually care about that. I am far more concerned with utility (which is where I think the "apply a species to a NPC statblock" falls down).
I think that the utility is fine, in that if you are about to run a session where your PCs face a horde of orcs, you have a ton of orcs to use. Sure, your standard "grunt" orcs are "toughs" but you have orc scouts, orc berserkers, orc cultists, orc guards, orc captains, etc. It's pretty versatile.
The only thing strange is that, aside from fluff (and the very probable addition of darkvision and maybe the old "agressive trait" (I'd add it, myself, but that's up to you) - it's the same session (mechanically) as if your PCs were raiding a small town of humans.
But the story is different, and all the RP would be different.
As I've said before, it's not how I would have done it if I were WotC (I'd go the other way and include Humans, Elves, Drow, Dwarves, Halflings, etc in the MM with at least four statblocks each and then tell people to mix'n'match 'em with a few simple swappable traits).
... But it's totally usable.