Those areas, as well as a handful more, all seem to be unfinished. The moonlit balcony, for example, is currently an inescapable dead end because the event that should let you back out into the room with the owl has been placed on the wrong event layer. As of 0.98c, the "under construction" signs have been removed from most of those hidden areas, but some of them, like the room with the clocks and the monochrome room with the eyeball, remain otherwise unchanged.
There have also been some major changes to the Dark Museum/Flying Fish World set of content in the game from 0.98b to 0.98c, so it's being worked on pretty extensively. I get the feeling the potted plant entrances in Flying Fish World are temporary, as there are a couple more that aren't normally accessible since their respective events are on a different event layer than the player.