EDIT: I have since found that the Digraphs package sometimes counts homomorphisms incorrectly. Perhaps this problem has been fixed in more recent versions though. I use Minion for counting homomorphisms instead.
The Digraphs package for GAP has several functions for finding homomorphisms of various types between graphs, including functions that will find all such homomorphisms, or all homomorphisms up to symmetries of the target graph. Once you have them all you can just count them to find the number. I really recommend this package, it seems to perform very well. For instance its chromatic number routine seems to be much faster than the chromatic number routine in SAGE.