Why is navigable correct?
I don't have an answer for why navigate yields navigable instead of navigatable; but in doing so, navigable is by no means a rule breaker among its closest peers. In fact, English has at least eight word pairs involving verbs with a -gate ending and adjectives with a -gable ending, as confirmed by The American Heritage Dictionary of the English Language, fifth edition (2010):
investigate --> investigable
irrigate --> irrigable
litigate --> litigable
mitigate --> mitigable
navigate --> navigable
obligate --> obligable
propagate --> propagable
segregate --> segregable
AHDEL doesn't list any similar -gable adjective form for a larger group of at least seventeen -gate verbs:
abrogate
aggregate
arrogate
castigate
conjugate
congregate
corrugate
delegate
derogate
elongate
fumigate
instigate
interrogate
relegate
subjugate
subrogate
supererogate
But on the other hand, it doesn't list any adjectives of the form -gatable. For these reasons, it seems fair to say that, within the subset of -able adjectives associated with verbs ending in -gate, navigable follows the standard pattern—the same one that the other seven -able adjectives associated with -gate verbs follow.