The following script works for me:
imp = IJ.openImage("http://imagej.nih.gov/ij/images/bat-cochlea-volume.zip");
stk = imp.getStack();
tst = stk.getVoxel(1,1,0);
print(tst); // prints 0
Are you sure your active image is a stack and has the correct dimensions?
If you keep having issues, maybe you can post a sample image that reproduces the problem?
That depends on what you want to achieve. In many cases, you don’t need to go down to the level of single pixel access, but you can use functions or filters that provide a high-level access.
Why don’t you tell us a bit more about your goals?