-n + chomp can be replaced with -nl.
That should be /\t/, I think? -a would be better than split
du -b */*/old.zip | perl -F\\t -lane'system zip => "-d", $F, "*exe* +"'
Or shorter and simpler yet:
du -b */*/old.zip | perl -ne'system zip => "-d", /\t(.*)/, "*exe*"'
My earlier comment on error checking still applies.