if your scripts process online payments or perform some encryption or some secretive stuff, it would be a nightmare scenario if your server allowed people to see your perl source instead of executing it

Only if your code is buggy or your security practices are bad. Granted it's certainly not desirable to give hackers a view of your code because they may notice weaknesses you did not or find shortcuts to making brute force attacks affordable but assuming correct code and proper practices, it makes no difference. If it did, all open source applications would be inherently insecure.