from what I can see, MAME/MESS makefile only explicitly gives dependencies for components which use no .h file (like most snes add-on chips and some model2/model3 video routines) and hence are directly included into other source files
otherwise, files got only compiled once without dependencies and at linking stage all the pieces are glued together. in this specific case, atari_vg.c is compiled in atari.a.
to make easier spotting subtle dependencies, in MESS makefile there is a shared.a entry which collects components used by multiple systems, but I'm not sure if MAME has one as well, neither if it makes sense to have it (in the sense that I'm not so sure shared.a would make easier the creation of tiny.mak to average users)
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