Lunch lady is the daughter of the lady in Dobuita. They've got two locations and you never see Hikasa in Dobuita. At least, I haven't. By the same token, her mother never goes to the harbor. Ryo probably doesn't know about Hikasa working the harbor location or didn't think to ask about it.
I'm not sure why this is so confusing. It's been pretty clear that to regular citizens who don't work there, the harbor is just the harbor. To people who work there, obviously they give the warehouse areas a nickname in the warehouse district. At my job, we have nicknames for things regular citizens wouldn't know about either.
This makes a lot of sense and you're just nitpicking the game.

Clearly Hikasa lives or lived in Dobuita because Ryo knows her. Its been established he doesn't know about anything outside of his town (even that is being generous to him) . If you have a chain of shops and your daughter runs one of them and you've never even seen the place you are both a bad mother and a bad businessman.
Just because the Tom gag is funny he knew about the warehouse district. Its also been established that people in both towns call it the warehouse district. People do travel between the places otherwise the bus would not be 30 mins apart. Every shop owner should at least be aware of the warehouse district because they get shipments or pick it up themselves from there in some cases.
Sure they can but not about something thats 2 min bus ride away.
also
Never!