Not trying to be mean, but Have you read the Apache Manual?
Relevant text:
Normally, if multiple Options could apply to a directory, then the
most specific one is used and others are ignored; the options are not
merged. (See how sections are merged.) However if all the options on
the Options directive are preceded by a + or - symbol, the options are
merged. Any options preceded by a + are added to the options currently
in force, and any options preceded by a - are removed from the options
currently in force.
It's a bit dense, but what it's saying is essentially "either will work, as long as there is no Options
directive later that overrides it". If you want to be certain, you should specify -Indexes
for each directory you want to protect.