Hardcoded "graphics" probably don't fall under copyright rules if they are generated algorithmically. The output of such an algorithm can probably be distributed safely, or the functionality of the algorithm could be replicated by various means.
However, if I understand correctly, copyright does extend to all content of an artifact (a game in this case), whatever form it might have. So even if the 3x3 px squares are hardcoded into an executable file bit by bit its form does not differ much from the representation it would have in a PCK or SPK file. Thus it is likely that it is covered by the same copyright terms as the rest of the game content.
I am quite sure we are free to
replicate (not
copy from the source) such
trivial graphics as a 3x3 px blob on our own if it does not breach a trademark (fx. this might be the case with the graphic update for The Two Sides due to the very specific replication of UFO:EU's characteristic character and vehicle design) or a patent (which would be next to impossible to achieve for the graphics themselves as patents are usually connected to processes of creating artifacts in non-trivial manners).
In terms of copyright it all comes down to whether you are "licensed" to distribute a work (or parts of it) created by another person/entity than yourself.
I am no expert in the field though
