The shaft represents a penis if a pestle represents a penis. The base represents a vagina if the mortar represents a vagina. If making chutney using mortar and pestle is same as doing sex, then yes Shiva Linga represents sex.

If holding the pestle while making aachar is same as holding a penis, then yes praying to Shiva Linga is praying to a penis.

Take a look at your fingers, they are same shape also. It is only your dirty mind at work.