Okay I should've gone into detail more, but the whole penis idea doesn't fit into the plot and doesn't make sense. First of all from a Christian perspective (Mr. Stoker was Protestant) that would be considered an evil thing to do. Since they are undead that would similar to necrophilia which is most definitely unChristian and would go against everything the book is talking about. Also remember, this book was written in 1897 which really wasn't that long ago. The whole idea of stakes being penises doesn't make sense as cleansing (I don't think Christians ever believed in cleansing the undead with their penis... EVER) so from a moral perspective it doesn't fit in the book.
Now here is what I should've said: Why a stake in the first place? Anyone who knows anything about a stake is that they hold things in place and hold them into the ground. What does the stake do? It keeps the vampire literally stuck into the coffin! It's like pinning insects to a board. This means that the vampire would not be able to escape at all. Also remember how the undead are between the living and the dead? Driving a stake through a vampire's heart and sticking them into the coffin is literally and metaphorically keeping them dead. They are stuck to their coffin so they may never escape death so metaphorically it is returning them to their grave so that they cannot walk again amongst the living. This fits with the whole purpose of them killing vampires. Their duty is to make sure vampires can't leave their graves and they pin them into their graves. This makes sense and fits with the plot.
Now are there some sexualized stuff in the book? Of course. Stoker obviously made the book a bit sexualized but sexualized doesn't mean speaking about sex. He was trying to show how Lucy was both terrifying and beautiful at the same time, but that is far from saying they were thinking sexual thoughts about her. So the whole penis thing really doesn't fit into the plot or even into historical reasoning. It doesn't have any backing as far as I have researched.