Hey there! There's currently no way to track your completion percentage, sorry. It's something we will definitely be adding, but it's a bit more difficult to do when the game is still a WIP, and new things are being added constantly.
To answer your specific questions in order, though:
-The 9th upgrade slot is impossible to earn at the moment, it will be added into the game later on.
-It's not possible to open the doors in the Subaquatic Station right now.
-It's also not possible to get through small openings in walls while underwater, since Alicia's movement options are more limited.
In general, there are a number of places in the game that currently don't lead to anything, or areas that are inaccessible - I understand that can be frustrating when you're trying to do everything the game has to offer, it's just an unfortunate consequence of the game still being in development. Those areas will be accessible and filled out eventually!