Thanks phranque, I'm not sure I understand this is related to my question. Even so I read the info and it is useful for me in other ways.
What I meant is if at any time server side includes fail just like php files on certain situations (not regarding a bad config). Using SSI would help me a lot to preserve the original html files with their sections being editable in Dreamweaver while the scripts are only scripts.
My solution to this today is to keep the html files as they are and create perl files who would only read and print those html files. Why? I want to avoid copying the text and creating the perl file itself with the html inside. Keeping separate files sure means x2 files but I can (or anybody) can edit the html file and then upload it back to the server.
As for security, I found on the links you provide me something very useful that goes kinda like this: "you can run perl scripts outside the server cgi-bin but in case of failure the source code might be revealed... so, store the perl files ONLY inside the cgi-bin". That's what I always do and will keep doing, this solves my question in many ways.
So at the end I will avoid SSI, will keep using perl inside the cgi-bin and will add mod rewrite to the formula to have site.com/page.htm instead of the long url.
Thanks, the info was very useful.