There is probalby a way to read through the scripts and indentify all the calls the make, but with all the diffrent ways to call subs in perl I can't imagin that it would be easy.
You might consider perl -d:DProf script.pl, as you noted it might not catch all the subs if you don't execute every code path, but it would probably be easyer than adding loging statments to each library function.