It represents Lord Shiva. Even if the whole body of Shiva was there, it would still include his penis, anus, testicles, heart, liver, everything. Just because one cannot see it does not mean it is not there. But one would be praying to Shiva. It is just a shape for Shiva. If the dirty mind wants to give a sexual meaning to all this then why not include Vishnu and Brahma as well?

What is Vishnu doing on the other  side of the goddess?. Your dirty mind thinks of the bumhole so Vishnu is doing her from behind. And Brahma is doing Vishnu from behind. This way you can convince yourself that the whole Shiva Linga is all about sex.

However if you bother to read about the different parts, what is being symbolised there is not sex. You are praying to this overall concept where Lord Shiva is supreme.