The only "problem" here is that SSL does not behave the way eggdrop expects. AFAIK there is no way to obtain a SSL user's true ident, unless you have root priviledge on the server.
The whole purpose of SSL is to give the client and server a very secure means of communication. The protocol doesn't demand it, but my take on SSL (I am certainly no expert) is that no way is the server going to compromise that security by handing out a client's true ident -- not, that is, in any decent implementation of SSL. As far as the rest of the world is concerned, the user is logged on to the server's localhost.
I didn't even know there were any SSL-enabled irc applications, client or server. What are these people using to join the server?
Of course a +c user flag isn't going to help you sort out the true idents of these people. Read .help common.
Probably you don't want your new users to default to having partyline access (+p) either -- for that matter, I wouldn't give a new user +fv, but that might be just me.
The script called automatic has lines in it for users with hostmask containing the characters "?" and "*" I altered these to include "irc" and "127.0.0" which is the case for indymedia's ssl connection.. we'll see if that does the job.