Yeah, you can do this without symlinks using the -f flag to "make", but I'm guessing that you want something more automatic.
I don't know of any automatic way to have a Makefile that is a global fallback for everything (if you take this idea to its natural conclusion, it doesn't really make sense anyway - you don't want your C code falling back to the LaTeX Makefile if it doesn't find a build rule).
So, yes and no. If you don't mind typing make -f /global/location/Makefile instead of just "make", then you don't need the symlinks. Otherwise, I would just stick with the current approach.
Actually, scratch that. I would *copy* the makefile into each directory so that if, sometime down the road, you want to rebuild your paper, you aren't dependent on the Makefile being super backward-compatible. Otherwise you might find that something that once built fine no longer does.
- C