It isn’t autotools syntax,it is just plain GNU make, and that syntax just sets the variable emu to 1 inside the make run, which is very useful for conditional compilation. So you could have something like this in a makefile
NVCCFLAGS := -g -I$(INCDIR) --compiler-options -fno-strict-aliasing -deviceemu
CFLAGS := -g -I$(CUDAHOME)/include -I$(INCDIR)
NVCCFLAGS := -I$(INCDIR) -arch sm_11 --compiler-options "-Wall -fno-strict-aliasing"
CFLAGS := -g -O0 -mtune=core2 -fPIC -I$(CUDAHOME)/include -I$(INCDIR)
which would set flags for compilation depending on whether you want device emulation or not.
As to the original question, that error means make can’t work out a rule to make a file which a target you are trying to build requires to compile. Make has a set of built-in rules for automagically deducing how to make dependencies, and the Makefile contains additional rule sets which replace or augment these built-in rules so it can build the target you want. The short, general answer is that the makefile is broken somehow.