It looks like you've already got the the optional arguments handled correctly in your subroutine, but you're passing it a hash reference where it expects a plain list. Change your subroutine invocation to:
StartCapture(
twigs => {filter => $filterTwig, capture => $captureTwig},
hashes => {filter => \%filterHash, capture => \%captureHash},
files => {filter => 'filter.txt', capture => 'capture.txt'},
results => 'c:/temp.txt'
);
Notice that I also changed %captureHash and %filterHash to \%captureHash and \%filterHash so they are passed as references instead of flattening into lists.
To access nested elements, you can do something like $args{twigs}{filter}. For more, see perlreftut and perldsc.
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