There are some famous jinja ceremonies that involve tall poles. The most famous is Suwa Taisha, in Nagano Prefecture, where four tree trunks are set up at the sanctuaries in a matsuri held once every six years. Naturally, some people have suggested that this is phallic symbolism.
I was reading a book on a different topic the other day, and it suggested that jinja as a whole were symbolic of the female reproductive organs. The torii is the vulva, the sacred path is the vagina (both are called “sandō” in Japanese, which obviously clinches it), and the sanctuary is the womb.
It is very common for a jinja to have multiple torii, typically passed through one after another as you approach the sanctuaries.
It is also common for jinja to have multiple sacred paths, approaching the sanctuaries from different directions. These paths also bend at many jinja, and it is not that uncommon for the sanctuaries to be off to one side, although Kashima Jingū, where the sanctuary is to the right of the sacred path soon after you pass through the torii, and the path keeps going, is an extreme case.
Finally, a substantial number of jinja have multiple sanctuaries; two at Shimogamo Jinja, for example, and four at Kasuga Taisha.
Basically, this symbolism might seem plausible if you only looked at the “standard jinja” diagrams in basic books about Shinto, but it fails completely if you look at actual jinja.
Besides, if jinja want to put images of sexual organs in the precincts, they just put images of sexual organs in the precincts.