Seems like it. I mean, they have different intro rooms, different enemies. Granted, there are lots of similar and shared assets between the two, but the paths through the game seem at a glance to be subtly different.
Granted, maybe they aren’t actually that distinct from each other, but there are definitely differences. Hacker9 has a different opening area and different characters tasking Snort. The introductory story segments upon starting a new game are entirely different, as they tell two different stories that don’t really seem to have anything but the faintest similarities. Even the levels that appear to be recycled between the two games, and these are definitely present, the challenges are quite different. I think Hacker9 has more weapons as well.
Hacker9 also appears to use Box2D physics, and has an expanded/annoying inventory system with all kinds of items to push around (some of which even boast a debatable gameplay value).
Yet to come is Ghost9 Solid (which may also go by the name Ghost94, which @loki wrote some about here), which looks to be a 2.5D take on the established storyline. Who knows whether that’ll be a gimmick or some serious business that takes advantage of the peculiarities of its chosen graphics format. From the video I have seen thus far though it looks as though it seems lamentably similar to a 3D engine for Super Mario World.
Nevertheless, I hold that Hack9 and Hacker9 are, indeed, two distinct games. If they weren’t then I dare say it’s a touch mysterious as to why the author would even bother.
Anywho, I will take a moment to compare the readme.txt files for both games though to see if there’s any indication as to what relationship the games have, outside of the obvious prequel/sequel relationship that I think they have. Hopefully I’ll know more after I get a controller here at the home and can really spend some time with these intriguing games.