You need to get nihistro from here
http://4dsdev.org/thread.php?pid=342#342 and put the exe's in /devkitPro/devkitARM/bin and you should be fine to compile.
got nihistro; this happened...
> "make"
shader.vsh
sf2d.c
arm-none-eabi-gcc -MMD -MP -MF /c/Users/User/Downloads/CTR_HB/sf2dlib-master/sf2dlib-master/libsf2d/build/sf2d.d -g -Wall -O2 -march=armv6k -mtune=mpcore -mfloat-abi=hard -I/c/Users/User/Downloads/CTR_HB/sf2dlib-master/sf2dlib-master/libsf2d/include -I/c/devkitPro/libctru/include -I/c/Users/User/Downloads/CTR_HB/sf2dlib-master/sf2dlib-master/libsf2d/build -DARM11 -D_3DS -c /c/Users/User/Downloads/CTR_HB/sf2dlib-master/sf2dlib-master/libsf2d/source/sf2d.c -o sf2d.o
c:/Users/User/Downloads/CTR_HB/sf2dlib-master/sf2dlib-master/libsf2d/source/sf2d.c:36:8: error: unknown type name 'aptHookCookie'
static aptHookCookie apt_hook_cookie;
^
c:/Users/User/Downloads/CTR_HB/sf2dlib-master/sf2dlib-master/libsf2d/source/sf2d.c: In function 'sf2d_init_advanced':
c:/Users/User/Downloads/CTR_HB/sf2dlib-master/sf2dlib-master/libsf2d/source/sf2d.c:79:2: warning: implicit declaration of function 'aptHook' [-Wimplicit-function-declaration]
aptHook(&apt_hook_cookie, apt_hook_func, NULL);
^
c:/Users/User/Downloads/CTR_HB/sf2dlib-master/sf2dlib-master/libsf2d/source/sf2d.c: In function 'sf2d_fini':
c:/Users/User/Downloads/CTR_HB/sf2dlib-master/sf2dlib-master/libsf2d/source/sf2d.c:104:2: warning: implicit declaration of function 'aptUnhook' [-Wimplicit-function-declaration]
aptUnhook(&apt_hook_cookie);
^
c:/Users/User/Downloads/CTR_HB/sf2dlib-master/sf2dlib-master/libsf2d/source/sf2d.c: In function 'sf2d_start_frame':
c:/Users/User/Downloads/CTR_HB/sf2dlib-master/sf2dlib-master/libsf2d/source/sf2d.c:154:19: error: 'GPU_STENCIL_KEEP' undeclared (first use in this function)
GPU_SetStencilOp(GPU_STENCIL_KEEP, GPU_STENCIL_KEEP, GPU_STENCIL_KEEP);
^
c:/Users/User/Downloads/CTR_HB/sf2dlib-master/sf2dlib-master/libsf2d/source/sf2d.c:154:19: note: each undeclared identifier is reported only once for each function it appears in
c:/Users/User/Downloads/CTR_HB/sf2dlib-master/sf2dlib-master/libsf2d/source/sf2d.c: In function 'apt_hook_func':
c:/Users/User/Downloads/CTR_HB/sf2dlib-master/sf2dlib-master/libsf2d/source/sf2d.c:284:14: error: 'APTHOOK_ONRESTORE' undeclared (first use in this function)
if (hook == APTHOOK_ONRESTORE) {
^
make[1]: *** [sf2d.o] Error 1
"make": *** [build] Error 2
> Process Exit Code: 2
> Time Taken: 00:10