Now that I think about it, how does one's smell STAY in the entry plug anyway? [...] how can you smell the pilot? :S
It is possible that the Eva units themselves retain the smell of their pilots on purpose
well, smell (like all the other senses) isn't necessarily about the nose itself, or the chemoreception of odorant substances, but about how the brain interprets those signals. when you're synched to an eva, your brain is basically connected to this giant robot, whose only discernible "mental" activity is coming from someone else's soul. it's likely that this connection enables the interpretation of signals of one being to intertwine with the other.
going off what o-san said, you wouldn't need to actually have odorant substances in the LCL if the soul within the eva can somehow send a signal to your brain telling you that you're smelling your mother. or smelling the previous pilot, or whoever. i guess it's kind of like how the pilot themself gets injured if the eva gets injured, depending on the level of synchronization.
in the case of mari while she's outside the eva, though... i don't know, she's just weird.
i like the idea that she somehow smells lilith on Shinji, though! can't be sure from her words whether it's that or whether it's something about Shinji himself, but it's nice speculation.