The way I see it is that people that have a 3DS and want 3D, updated controls, and new features will go with Snake Eater 3D.
The people that have a PS3/Xbox 360/Vita that want HD graphics will obviously go for the HD collection.
Get where I'm going? I suppose people that already own both systems like me may be in a bind, but ultimately a lot of people will be getting both, if they have both consoles of course. I, personally, have all the next gen consoles, so I'll be getting Snake Eater 3D, and the HD Collection.
Snake Eater 3D is of course in 3D, has updated controls, has a couple new features and maybe a couple more that have yet to be revealed!
The HD Collection has remastered HD ports, so I'll be getting those for the pretty graphics and of course for the collection! I wont be getting Snake Eater with updated controls, and new features, but that's why I have Snake Eater 3D, right?
My point is that the HD collection releasing before Snake Eater 3D doesn't really harm sales, at least not significantly. Snake Eater 3D is for the 3DS, an updated game, HD Collection is for the HD consoles, straight pretty ports. A lot of people will be getting both, I'm proof of that!
That's how I see it, imo.