Well then Bonn will stay a village. We call it "Bundesdorf" for a reason

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Frankfurt will see a further increase in population, population density and areal expansion. Smaller cities around Frankfurt in southern Hessen and northern Bavaria might see an increase in population as well and some might get a federal agency or two.
Governmental shelters, bunkers and redoubts would be situated in the Taunus and maybe the Odenwald instead of the Eifel.
AFAIK it was more or less Adenauer's choice to make Bonn the capital as it was in close proximity of his beloved Cologne.
OTOH Frankfurt is much more vulnerable to a soviet assault on West Germany. The allied occupying powers always thought of the
"Fulda Gap" as the most likely invasion route for a soviet army and from their to Frankfurt it would be at most a two day trip for the Red Army.
Would the capital be moved to Berlin?
Technically Berlin was always the capital of Germany since 1871, Bonn was only "Regierungssitz" (seat of Government) much like The Hague and Amsterdam in the Netherlands.
So yes, probably they will transfer all the ministries and agencies to Berlin after a reunification.
But maybe as Frankfurt is far more prestigious as Bonn parlament may decide otherwise. I guess IOTL they voted for Berlin not only as a symbol for unity but also because it simply was the biggest german city.