No real secret areas, but if you get those jumpboots in the same house with the flak cannon, you can explore the attics.
Push the little stone sticking out of the wall, then take a right and at the end of the hall turn left. When you go up the elevator there should be 2 monk statues. Push them both out the window causing them to break, leaving you some items. (If they randomly stop when you're pushing them, then start shooting.)
The nalighost under the grave yard opens tombstones containing lots of items (refer to secret below)
The nalis in the church will open two doors for you.
Okay, press the the part of the grave which i've shot to open the large tombstone at the end of the grave yard to reveal a lift. While going down there is a small area with ammo before you reach the very bottom. At the the very bottom is a nali ghost which will open a variety of tombstones containing lots of goodies!
Take the straight pathway, then stop (leads to picture below)
Shoot the circled area.
In case the picture wasn't enough, these are the stairs leading to the church. Jump on the torch and a square in the floor will open right next to the bottom of the staircase.
Follow the red trail, then shoot the circled area.