How to prepare squid to avoid spermataphores
Based on the article SAJ14SAJ linked to in the comments, in the only known case in which this happened with cooked squid, it was parboiled, and almost certainly not fully cooked: "the whole squid spent just a few seconds in boiling water". If the squid is cooked, then the spermatophore will be inactive, and nothing bad is going to happen. (Living things tend to stop moving once they're cooked and dead.)

If you're trying to completely safely eat raw squid, I expect you need some squid anatomical knowledge which I don't have, so you'll want to wait for another answer.