it make sense to modify my application so that worker perl scripts are invoked via do() instead of system calls?
Giving bad advice is difficult to avoid if the situation isn't clear, in this case: of what kind are the performance issues? Memory, responsiveness, load of the server?
do file reads a file and executes it. That happens in an unrelated scope with regards to the main script, but that can stomp on global variables or those declared with our, re-define subroutines and whatnot. So all of these 500+ scripts must be revised to check these issues before executing them via do.
Having done that, I would make each script into a file containing just a distinct subroutine, and have them executed via AutoLoader. See POSIX for an example. If memory is an issue, I'd use AutoReloader, keep track of invocation time and memory usage, and periodically unload (via an alarm handler) those scripts (now subroutines) which are seldom used and/or cause the most memory impact.
perl -le'print map{pack c,($-++?1:13)+ord}split//,ESEL'