The game developers have already give players the exploration tools to find secret areas, all you gotta do is just upgrade it and go to places to find it.
Secret Area Locations
Sewer Boss Location
Come back to the boss location after defeating the boss.
Then move right and you will see chests in the room.
Sewer (Pink Water Area)
Go to top right of pink water where you can see two chest just before you about to step out of the water.
There is a secret path that leads to a boss guarding a chest.
Renegade Bar Area 3F
Go hug on the wall right of this room.
There will a path in the middle of the wall near the trashes that leads to a chest.
Renegade Base 4F
Start from the staircase to 4F.
Then walk to the first room you see, there will be lone red renegade in the room.
Then go hug the wall on the right of screen (near 2 sofa with a table) there will be invisible black entrance to another room with a boss guarding a chest.