Assuming your question is in regard to:

Also, if your problem allows you to unpack the strings just in time at the point where you need them, rather than en masse, avoiding the allocation, creation and destruction of 10 million concurrent small arrays -- even if you have ample memory for them -- can save a significant amounts of time.

I meant -- unpack the strings just in time at the point where you need them -- something like:

for my $seq ( @seqs ) {
    my @bits = unpack 'a3a3a3', $seq;
    ## $bits[ ... ]; 
}
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rather than -- en masse --:

@seqs = map[ unpack '(a3)*', $_ ], @seqs;
for my $ref ( @seqs ) {
    ## $ref->[ ... ]
}
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At it again. Unannounced updates. The above post originally consisted entirely of just:

Any implementation in mind? Something like the following?

while ($seq =~ /(.{3})/sg) {
   # Substring in $1
   ...
}
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To answer the dumb question that wasn't there originally,

How can you not know in advance how many fields there are (int(length($seq)/3))?

If you have to calculate the number, you throw away the few percent gained.