Of course they do...
Footprint analysis is simply programming site and distribution signatures into their algo'.
They can they apply weighting to link juice according to the site type, distribution and setup.
Google's algo seems to use over 200 factors now, and it will be more complex than any one person could understand. With modern linking techniques, google HAS to use this technique to control all the link-farms etc. it's one of the reasons why panda slapped article directories and middle-man sites so hard.
We just have to get ever more creative with how we build links and link structures... And avoid systems that leave large foot-prints.